About NTRK1
No gene-level summary was recorded for this case.
Previous versions
Variant interpretation report
NTRK1 c.1999G>A, p.(Gly667Ser)
Classification
Uncertain significance
Variant description:
No variant summary was recorded for this case.
Five-step scale from benign to pathogenic. This variant is uncertain. Select a step to read what it means.
Uncertain.The recorded classification is uncertain significance.
In plain language
Gene-level background from the recorded interpretation.
Words with a dotted underline have a short definition. Hover or tap them.
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Criteria may be applied incorrectly, sources may be misread, and a
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Double-check every criterion and its underlying evidence
before relying on any call.
01The reasoning
How it was classified
The recorded framework is Not recorded. The criteria and strengths shown below come from the saved assessment; this page does not recalculate the classification.
Recorded applied criteria
The applied criteria and their strengths are shown as assessed under the stated framework.
Pathogenic evidence criteria: 2
Benign evidence criteria: 0
Pathogenic criteria applied · 2
PM1Moderate
PM1 · moderate
The variant alters Gly667, which is the xDFG residue immediately N-terminal to the DFG motif (Asp668-Phe669-Gly670) in the activation loop of the NTRK1 tyrosine kinase domain. The DFG motif is a critical, evolutionarily conserved structural element that governs kinase conformational state (DFG-in active vs DFG-out inactive). PMID:33004339 demonstrates that xDFG substitutions at G667 (including G667S) emerge as clinical resistance mutations to type I TRK inhibitors and alter kinase-inhibitor interactions via in silico modeling. PMID:33328556 confirms altered drug binding for G667S across five kinase inhibitors by molecular docking. This residue lies within a well-characterized, functionally critical domain without known benign variation.
PM2Moderate
PM2 · moderate
NM_002529.3:c.1999G>A is absent from gnomAD v2.1 (exomes), gnomAD v4.1 (exomes), and gnomAD-Canada v1.0 (genomes). The variant has not been observed in any population database, consistent with PM2 at the <0.1% allele frequency threshold for a rare disease gene.
Benign criteria applied · 0
No benign criterion marked as applied in the recorded assessment.
Recorded classification: Uncertain significance
gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PM1 moderate, PM2 moderate; combination = 2 moderate, which maps to VUS.
02The sources
Evidence at a glance
Evidence summaries and captured source records, where available. Missing entries should not be interpreted as negative findings.
gnomAD v4.1
gnomAD v2.1
Population frequency
Not recorded
gnomAD v4.1 allele counts were not recorded for this variant.
gnomAD v2.1
Absent from gnomAD v2.1.
gnomAD-Canada
Absent from gnomAD-Canada v1.0.
SpliceAI score
0.160 maximum delta
Recorded SpliceAI maximum delta score: 0.160. Refer to the recorded PP3/BP4 rationale for interpretation.
No listed criterion applied
SpliceAI ↗
ClinVar submissions
Not recorded
A ClinVar laboratory submission summary was not recorded.
Context only
ClinVar ↗
Functional evidence
Statement recorded
OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Inconclusive; curated oncogenicity label: Inconclusive.
No listed criterion applied
OncoKB ↗
COSMIC
Cancer Hotspots
Somatic evidence
No matching record reported
This variant has not previously been reported in somatic cancers (COSMIC).
Cancer Hotspots
This variant does not lie in a statistically significant hotspot.
Context only
For specialists
Technical detail
ACMG/AMP criteria under Not recorded, with the data and sources behind each one.
26 criteria with recorded statuses: 2 met · 20 not met · 0 not assessed · 4 not applicable. Open any row for the full reasoning, the rule and the evidence behind it.
Met
Not met
Not assessed
Not applicable
NM_002529.3:c.1999G>A (p.Gly667Ser) is a novel missense variant in the NTRK1 gene. It is absent from population databases (gnomAD v2.1, v4.1, gnomAD-Canada; PM2) and is located in the functionally critical xDFG motif of the tyrosine kinase domain immediately N-terminal to the DFG activation loop (PM1). In silico data from two publications (PMID:33004339, PMID:33328556) demonstrate altered kinase inhibitor binding for G667S by molecular docking and molecular dynamics simulations, and G667S has been observed as an acquired somatic resistance mutation in two patients with TRK fusion-positive cancers on larotrectinib therapy (PMID:33004339). No experimental functional characterization of G667S exists, and the variant has not been reported in ClinVar. In silico predictors are discordant (REVEL 0.752, BayesDel 0.262).
Two moderate pathogenic criteria are met (PM1, PM2). Under the generic ACMG/AMP 2015 framework (Richards et al., PMID:25741868), this does not reach the threshold for Likely Pathogenic (which requires ≥3 moderate criteria, or ≥1 strong + ≥1 moderate, or ≥2 moderate + ≥2 supporting). No benign criteria are met. The variant is classified as a Variant of Uncertain Significance (VUS).
No criteria match.
Met · 2
PM1 ModerateThe variant alters Gly667, which is the xDFG residue immediately N-terminal to the DFG motif (Asp668-Phe669-Gly670) in the activation loop of the NTRK1 tyrosine kinase domain. The DFG motif is a critical, evolutionarily conserved structural element that governs kinase conformational state (DFG-in active vs DFG-out inactive). PMID:33004339 demonstrates that xDFG substitutions at G667 (including G667S) emerge as clinical resistance mutations to type I TRK inhibitors and alter kinase-inhibitor interactions via in silico modeling. PMID:33328556 confirms altered drug binding for G667S across five kinase inhibitors by molecular docking. This residue lies within a well-characterized, functionally critical domain without known benign variation. Details ▾Hide ▴
Evidence considered
- G667 is the xDFG residue in the NTRK1 kinase activation loop
- critical for kinase conformation. Altered inhibitor binding demonstrated in silico. Clinical emergence as somatic resistance mutation confirms functional importance.
Sources
PM2 ModerateNM_002529.3:c.1999G>A is absent from gnomAD v2.1 (exomes), gnomAD v4.1 (exomes), and gnomAD-Canada v1.0 (genomes). The variant has not been observed in any population database, consistent with PM2 at the <0.1% allele frequency threshold for a rare disease gene. Details ▾Hide ▴
Evidence considered
- Absent from gnomAD v2.1 (AC=0). Absent from gnomAD v4.1 (AC=0). Absent from gnomAD-Canada v1.0 (AC=0
- AN=0).
Sources
Not met · 20 · evaluated, threshold not reached
PS2 No de novo observation data are available for this variant. No reports of de novo occurrence with confirmed parentage were identified in the case materials or literature. Details ▾Hide ▴
Evidence considered
- No de novo data available.
Still missing
- No parental testing or de novo confirmation data available.
PS3 No experimental functional data exist for NM_002529.3:c.1999G>A (p.G667S) relevant to germline disease mechanism. PMID:33004339 includes G667S in molecular dynamics simulations (in silico modeling) and reports its emergence as a somatic resistance mutation in two patients with TRK fusion-positive cancers on larotrectinib, but no wet-lab functional assay (kinase assay, reporter assay, or other experimental characterization) was performed specifically on G667S. PMID:33328556 provides molecular docking dissociation constants for G667S (in silico only). Computational predictions do not satisfy PS3 requirements for experimental functional evidence. The somatic resistance context does not inform germline NTRK1 loss-of-function pathogenicity for CIPA. Details ▾Hide ▴
Evidence considered
- G667S studied by in silico molecular docking and MD simulations only
- no experimental functional assay for this variant. G667C (same residue
- different substitution) was experimentally characterized but does not establish effect of serine substitution.
Still missing
- No experimental functional characterization of p.G667S in any assay system.
Sources
PS4 No case-control or cohort data comparing variant prevalence in affected individuals versus controls are available. The variant has been observed as a somatic resistance mutation in two cancer patients (PMID:33004339), but this does not constitute germline case-control evidence for PS4. Details ▾Hide ▴
Evidence considered
- No germline case-control data available.
Still missing
- No affected-vs-control prevalence data for germline disease.
PM5 No missense variant at codon 667 resulting in a different amino acid substitution has been classified as germline pathogenic in ClinVar. G667C has been reported as a somatic resistance mutation in TRK fusion-positive cancers (PMID:33004339, PMID:33328556) but is not classified as germline pathogenic. The PM5 candidate search found zero same-residue comparator variants in ClinVar. Details ▾Hide ▴
Evidence considered
- No germline pathogenic missense at same residue in ClinVar. G667C is a somatic resistance variant
- not germline pathogenic.
Sources
PM6 No de novo observation data are available. PM6 (assumed de novo without confirmation of paternity and maternity) cannot be applied without at least one report of a de novo occurrence. Details ▾Hide ▴
Evidence considered
- No de novo data available.
Still missing
- No de novo reports identified.
PP1 No segregation data are available for this variant. No family studies with affected and unaffected members have been reported. Details ▾Hide ▴
Evidence considered
- No segregation data available.
Still missing
- No family segregation analysis.
PP2 The HCI prior score is not available for NTRK1 (gene_not_supported), and no missense constraint Z-score or benign missense depletion data were provided in the evidence packet. Without evidence of a low rate of benign missense variation, PP2 cannot be applied. Details ▾Hide ▴
Evidence considered
- HCI prior not available for NTRK1. No missense constraint data.
Still missing
- Missense constraint (Z-score) data not available for NTRK1.
PP3 In silico predictions are mixed and do not provide multiple concordant lines of evidence for a deleterious effect. REVEL score is 0.752 (moderately elevated above 0.5, leaning pathogenic), but BayesDel_noAF score is 0.262 (low, leaning benign). SpliceAI max delta score is 0.16, predicting no significant splice impact. The discordance between REVEL and BayesDel prevents application of PP3, which requires multiple lines of computational evidence agreeing on a deleterious effect. Details ▾Hide ▴
Evidence considered
- REVEL=0.752 (leaning pathogenic). BayesDel=0.262 (leaning benign). SpliceAI max_delta=0.16 (no splicing impact). Predictors are discordant.
Sources
PP4 No patient phenotype or clinical data were provided with this case. The variant cannot be matched to a specific clinical presentation without phenotypic information. Details ▾Hide ▴
Evidence considered
- No patient phenotype data available.
Still missing
- Patient phenotype information not provided.
PP5 NM_002529.3:c.1999G>A is absent from ClinVar. No reputable source has classified this variant as pathogenic. PP5 requires a ClinVar entry or equivalent authoritative classification, which does not exist for this variant. Details ▾Hide ▴
BA1 The variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada. Allele frequency is 0%, far below the BA1 threshold of >1% (or >5% per ACMG 2015). Details ▾Hide ▴
BS1 The variant is absent from all population databases. Allele frequency is 0%, far below the BS1 threshold of >0.3% for a rare autosomal recessive disorder expected at very low frequency. Details ▾Hide ▴
BS2 The variant has not been observed in any individual, healthy or affected, in population databases or published cohorts. No observation in a healthy adult is available to support BS2. Details ▾Hide ▴
Evidence considered
- Variant not observed in any population database.
Still missing
- No observation in healthy controls.
Sources
BS3 No well-established in vitro or in vivo functional studies demonstrate a benign effect for p.G667S. No experimental functional data of any kind exist for this specific variant beyond in silico modeling. Details ▾Hide ▴
Evidence considered
- No experimental functional studies exist for G667S. In silico data show altered inhibitor binding
- not a benign effect.
Still missing
- No benign functional evidence.
Sources
BS4 No segregation data are available to assess lack of segregation with disease in affected family members. Details ▾Hide ▴
Evidence considered
- No segregation data available.
Still missing
- No family segregation data.
BP1 NTRK1-related CIPA (congenital insensitivity to pain with anhidrosis) is caused by both missense and truncating loss-of-function variants. Over 105 NTRK1 mutations have been reported in CIPA, many of which are missense (PMID:30201336). BP1 requires that the gene primarily cause disease through truncating variants, which is not the case for NTRK1. Details ▾Hide ▴
Evidence considered
- CIPA is caused by both missense and truncating NTRK1 mutations. Missense is a known disease mechanism.
Sources
pvs1_gene_context
BP2 No phasing or trans-configuration data are available. BP2 requires observation of the variant in trans with a pathogenic variant in a fully penetrant dominant disorder, or in cis with a pathogenic variant in a recessive disorder. Neither configuration has been assessed for this variant. Details ▾Hide ▴
Evidence considered
- No phasing data available.
Still missing
- No trans/cis configuration data.
BP4 Computational evidence is mixed and does not provide multiple concordant lines suggesting no impact. SpliceAI max delta is 0.16 (predicting no splice effect), but REVEL is 0.752 (elevated, leaning pathogenic), and BayesDel is 0.262 (leaning benign). The discordance among predictors prevents a clear conclusion of no impact. BP4 requires multiple lines of computational evidence to agree on a benign effect. Details ▾Hide ▴
Evidence considered
- SpliceAI=0.16 (benign)
- but REVEL=0.752 (not benign) and BayesDel=0.262 (equivocal). Discordant predictors.
Sources
BP5 No data are available indicating that the proband has an alternate molecular basis for disease. BP5 requires a co-occurring pathogenic variant in a different gene that fully explains the phenotype. Details ▾Hide ▴
Evidence considered
- No alternate molecular basis identified.
Still missing
- No proband genotype or alternate molecular basis data.
BP6 NM_002529.3:c.1999G>A is absent from ClinVar. No reputable source has classified this variant as benign. BP6 requires a ClinVar entry or equivalent authoritative benign classification. Details ▾Hide ▴
Not applicable · 4· recorded as not applicable Show reasons ▾Hide reasons ▴
PVS1 N/ANM_002529.3:c.1999G>A is a missense variant (p.Gly667Ser). It does not fall into the generic PVS1 null-variant buckets of nonsense, frameshift, or canonical ±1,2 splice consensus variants. PVS1 is not applicable to missense variants under the ClinGen SVI PVS1 framework (PMC6185798). Details ▾Hide ▴
Evidence considered
- Missense variant
- variant_bucket=other
- apply_generic_pvs1_framework=false.
Sources
pvs1_variant_assessmentpvs1_generic_framework ↗
PS1 N/ANo known pathogenic missense variant at codon 667 producing the same amino acid change (p.Gly667Ser) via a different nucleotide change has been identified. This variant is absent from ClinVar, and no alternate nucleotide substitution at this codon yielding p.Gly667Ser has been reported as pathogenic. Details ▾Hide ▴
Evidence considered
- Variant absent from ClinVar
- no same-amino-acid comparator identified.
Sources
clinvar ↗pm5_candidates
BP7 N/ANM_002529.3:c.1999G>A is a missense variant (p.Gly667Ser), not a synonymous variant. BP7 applies only to synonymous variants with no predicted splice impact and low nucleotide conservation. Details ▾Hide ▴
Evidence considered
- Missense variant
- not synonymous.
PS5 N/APS5 is not a standard ACMG/AMP 2015 criterion and is not defined in the generic ACMG classification framework used for this assessment. No VCEP-specific PS5 rule exists for NTRK1. Details ▾Hide ▴
Evidence considered
- Not a criterion in the applicable ACMG/AMP 2015 generic framework.
Sources
generic_acmg_combination_rulesfinal_classification_framework
Identifiers
- Gene
- NTRK1
- Transcript
- NM_002529.3
- Coding (HGVS c.)
- NM_002529.3:c.1999G>A
- Protein (HGVS p.)
- NP_002520.2:p.(Gly667Ser)
- GRCh38
- chr1:156879315 G>A
- GRCh37
- chr1:156849107 G>A
Gene diagram
Every interpreted variant in NTRK1, mapped onto the exon structure of NM_002529.3. Select a row to find it on the plot.
NTRK1NM_002529.3
Fetching transcript structure from UCSC…
Exons
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Transcript span
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Strand
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Variants mapped
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Source
UCSC ncbiRefSeqCurated
All variants in NTRK1
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Select a row to find it on the plot; use the link to open its page.
| Protein | Location | Classification | Link |
|---|
gnomAD v4.1
Allele count data not recorded
gnomAD v2.1
Allele count data not recorded
gnomAD-Canada v1.0
Allele count data not recorded
Statements
gnomAD v4.1
Absent from gnomAD v4.1.
gnomAD v2.1
Absent from gnomAD v2.1.
gnomAD-Canada
Absent from gnomAD-Canada v1.0.
SpliceAI and Pangolin
Other predictors
- REVEL
- 0.752
- BayesDel
- 0.262
How the predictions were used
PP3 In silico predictions are mixed and do not provide multiple concordant lines of evidence for a deleterious effect. REVEL score is 0.752 (moderately elevated above 0.5, leaning pathogenic), but BayesDel_noAF score is 0.262 (low, leaning benign). SpliceAI max delta score is 0.16, predicting no significant splice impact. The discordance between REVEL and BayesDel prevents application of PP3, which requires multiple lines of computational evidence agreeing on a deleterious effect. Details ▾Hide ▴
Evidence considered
- REVEL=0.752 (leaning pathogenic). BayesDel=0.262 (leaning benign). SpliceAI max_delta=0.16 (no splicing impact). Predictors are discordant.
Sources
BP4 Computational evidence is mixed and does not provide multiple concordant lines suggesting no impact. SpliceAI max delta is 0.16 (predicting no splice effect), but REVEL is 0.752 (elevated, leaning pathogenic), and BayesDel is 0.262 (leaning benign). The discordance among predictors prevents a clear conclusion of no impact. BP4 requires multiple lines of computational evidence to agree on a benign effect. Details ▾Hide ▴
Evidence considered
- SpliceAI=0.16 (benign)
- but REVEL=0.752 (not benign) and BayesDel=0.262 (equivocal). Discordant predictors.
Sources
BP7 N/ANM_002529.3:c.1999G>A is a missense variant (p.Gly667Ser), not a synonymous variant. BP7 applies only to synonymous variants with no predicted splice impact and low nucleotide conservation. Details ▾Hide ▴
Evidence considered
- Missense variant
- not synonymous.
Statement
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.16). REVEL score = 0.752. BayesDel score = 0.262014.
4 paper records listed. 2 cited in the classification.
Cited in the classification
-
PMID 33004339 ↗TRK xDFG Mutations Trigger a Sensitivity Switch from Type I to II Kinase Inhibitors.TRKA G667S emerged as an acquired resistance mutation in two patients with TRK fusion-positive cancers on larotrectinib: Patient 4 with TPR-NTRK1 non-small cell lung cancer and Patient 5 with TPM3-NTRK1 thyroid cancer. Both patients showed intrinsic resistance to the second-generation inhibitor selitrectinib. G667S was included in molecular dynamics simulations of TRKA xDFG mutants. In vitro kinase assays were performed on G667C and G667A but not on G667S.→ PM1 Names this variant
Source detail
Patient 4 with a TPR-NTRK1-positive non-small cell lung cancer had a partial response (PR) on larotrectinib. Sequencing of cfDNA at progression identified the emergence of TRKA G667S.
Location Results, paragraph on TRKA xDFG mutations (Patients 4 and 5); Methods, Structure Preparation section
Context Cell-free DNA sequencing from clinical samples; molecular dynamics simulations; in vitro kinase assays (G667C and G667A only, not G667S)
-
PMID 33328556 ↗NTRK kinase domain mutations in cancer variably impact sensitivity to type I and type II inhibitors.NTRK1 G667S was evaluated by molecular docking in both DFG-in (active) and DFG-out (inactive) kinase conformations. Dissociation constants showed reduced larotrectinib affinity in the DFG-in state (Kd 535.9 nM vs 100.9 nM wild-type), reduced entrectinib affinity (Kd 45.3 nM vs 4.6 nM wild-type), and paradoxically enhanced foretinib affinity in the DFG-out state (Kd 17.4 nM vs 54.3 nM wild-type). The study did not perform in vitro kinase assays or cell-based experiments on G667S; experimental work focused on G667C, V573M, and F589L.→ PM1 Names this variant
Source detail
G667S variant dissociation constants in Table 1: larotrectinib Active=535.9 nM, Inactive=2265.4 nM; entrectinib Active=45.3 nM, Inactive=147.1 nM; altiratinib Active=377.2 nM, Inactive=81.7 nM; cabozantinib Active=689.2 nM, Inactive=116.3 nM; foretinib Active=350.2 nM, Inactive=17.4 nM.
Location Table 1 (Dissociation constants); Results section
Context Molecular docking and homology modeling of NTRK1 kinase domain; Ba/F3 cell viability assays and immunoblotting performed for G667C, V573M, and F589L but not G667S
Other recorded publications
-
PMID 29466156 ↗Efficacy of Larotrectinib in TRK Fusion-Positive Cancers in Adults and Children.Reports the efficacy of larotrectinib in 55 patients with TRK fusion-positive cancers across adult and pediatric populations. The study concerns gene fusions involving NTRK1, NTRK2, and NTRK3. The specific point mutation NM_002529.3:c.1999G>A (p.G667S) was not reported or evaluated in this paper.Does not name this variant
-
PMID 30624546 ↗Larotrectinib in adult patients with solid tumours: a multi-centre, open-label, phase I dose-escalation study.Phase I dose-escalation study of larotrectinib in adult patients with solid tumors harboring NTRK gene fusions. The specific point mutation NM_002529.3:c.1999G>A (p.G667S) was not reported or evaluated in this paper.Does not name this variant
Screenshots represent source records captured during evidence collection. Select one to view the recorded source content.
gnomAD v4.1
Captured gnomAD v4.1 source record
Open source ↗
gnomAD v2.1
Captured gnomAD v2.1 source record
Open source ↗
SpliceAI Lookup
Recorded maximum delta 0.160
Open source ↗
ClinVar
Captured ClinVar source record
Open source ↗
COSMIC
Captured COSMIC source record
Open source ↗
Cancer hotspots
Captured Cancer Hotspots source record
Open source ↗
OncoKB
Captured OncoKB source record
Open source ↗
All source links
- ClinVar ↗www.ncbi.nlm.nih.gov/clinvar/?term=NM_002529.3%3Ac.1999G%3EA
- gnomAD v2.1 ↗gnomad.broadinstitute.org/variant/1-156849107-G-A?dataset=gnomad_r2_1
- gnomAD v4.1 ↗gnomad.broadinstitute.org/variant/chr1-156879315-G-A?dataset=gn…
- gnomAD-Canada ↗http://192.168.4.76:8001/variant/1-156879315-G-A
- SpliceAI Lookup ↗spliceailookup.broadinstitute.org/#variant=NM_002529.3%3Ac.1999…
- OncoKB ↗www.oncokb.org/gene/NTRK1/G667S
- COSMIC ↗cancer.sanger.ac.uk/cosmic/search?q=NTRK1+c.1999G%3EA
- Cancer hotspots ↗www.cancerhotspots.org/
Statements for reports
The evidence statements recorded by the interpretation pipeline. They have not been reinterpreted by the page.
gnomAD v4.1
Absent from gnomAD v4.1.
gnomAD v2.1
Absent from gnomAD v2.1.
gnomAD-Canada
Absent from gnomAD-Canada v1.0.
ClinVar
This variant is absent from ClinVar.
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.16). REVEL score = 0.752. BayesDel score = 0.262014.
Functional
OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Inconclusive; curated oncogenicity label: Inconclusive.
Somatic
This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).
Cancer Hotspots
This variant does not lie in a statistically significant hotspot.