About NOTCH3
No gene-level summary was recorded for this case.
Previous versions
Variant interpretation report
NOTCH3 c.4688C>T, p.(Pro1563Leu)
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.
LYFE Sciences is an AI system, and it can make mistakes.
Criteria may be applied incorrectly, sources may be misread, and a
confident-looking classification can still be wrong.
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: 1
Benign evidence criteria: 1
Pathogenic criteria applied · 1
PM2Supporting
PM2 · supporting
NM_000435.2:c.4688C>T is absent from gnomAD v2.1 (0/242,354 alleles) and observed at an ultra-rare frequency in gnomAD v4.1 (1/1,602,340 alleles; AF=6.24e-7), well below the 0.1% threshold for PM2_Supporting in the generic ACMG/AMP framework.
Benign criteria applied · 1
BP4Supporting
BP4 · supporting
Multiple lines of computational evidence support a benign impact. REVEL score is 0.08 (below 0.5 threshold), BayesDel score is -0.37 (below pathogenic threshold), and SpliceAI predicts no splicing impact (max delta = 0.00). All three in silico predictors are consistent with a benign or neutral effect.
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: PM2 supporting, BP4 supporting benign; combination = 1 supporting + 1 supporting benign, 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
1 / 1,602,340 alleles
gnomAD v4.1: 1 / 1,602,340 alleles. Recorded AF 6.24087e-07. Recorded homozygote count 0.
gnomAD v2.1
This variant is present in gnomAD v2.1 (AF= 0; MAF= 0.00000%, 0/242354 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 0; MAF= 0.00000%, 0/15004 alleles, homozygotes = 0).
SpliceAI score
0.000 maximum delta
Recorded SpliceAI maximum delta score: 0.000. Refer to the recorded PP3/BP4 rationale for interpretation.
ClinVar submissions
Not recorded
A ClinVar laboratory submission summary was not recorded.
Context only
ClinVar ↗
Functional evidence
Statement recorded
OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. NOTCH3 encodes a Type I transmembrane protein of the Notch family. Missense and nonsense mutations in NOTCH3 have been identified in various cancers.
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 · 10 not met · 9 not assessed · 5 not applicable. Open any row for the full reasoning, the rule and the evidence behind it.
Met
Not met
Not assessed
Not applicable
NM_000435.2:c.4688C>T (p.Pro1563Leu) is a missense variant in NOTCH3. It is absent from gnomAD v2.1 (0/242,354 alleles) and ultra-rare in gnomAD v4.1 (1/1,602,340 alleles; AF=6.24e-7), meeting PM2_Supporting.
Multiple computational predictors indicate a benign impact: REVEL score 0.08, BayesDel score -0.37, and SpliceAI max delta 0.00. This meets BP4 (supporting benign).
The variant is a missense substitution (not a null variant), so PVS1 is not applicable. It alters a non-cysteine residue (Pro1563) in EGF-like repeat 30, where the majority of established pathogenic NOTCH3 variants affect conserved cysteine residues; PM1 is not met.
The variant is absent from ClinVar and has no reported functional studies, de novo observations, case-control data, or family segregation data. OncoKB classifies it as 'Unknown Oncogenic Effect.'
In the generic ACMG/AMP 2015 framework, the current evidence yields PM2_Supporting and BP4_Supporting_Benign. These criteria are insufficient for a definitive classification; the variant remains a Variant of Uncertain Significance (VUS) pending additional clinical and functional data.
No criteria match.
Met · 2
PM2 SupportingNM_000435.2:c.4688C>T is absent from gnomAD v2.1 (0/242,354 alleles) and observed at an ultra-rare frequency in gnomAD v4.1 (1/1,602,340 alleles; AF=6.24e-7), well below the 0.1% threshold for PM2_Supporting in the generic ACMG/AMP framework. Details ▾Hide ▴
Evidence considered
- gnomAD v2.1: 0 alleles out of 242
- 354 (AF=0.0%)
- gnomAD v4.1: 1 allele out of 1
- 602
- 340 (AF=0.0000624%)
- gnomAD-Canada: absent (0/0 alleles
- no data available)
Sources
BP4 SupportingMultiple lines of computational evidence support a benign impact. REVEL score is 0.08 (below 0.5 threshold), BayesDel score is -0.37 (below pathogenic threshold), and SpliceAI predicts no splicing impact (max delta = 0.00). All three in silico predictors are consistent with a benign or neutral effect. Details ▾Hide ▴
Evidence considered
- REVEL score: 0.08 (benign-leaning)
- BayesDel score: -0.37 (benign-leaning)
- SpliceAI max delta: 0.00 (no predicted splicing impact)
Sources
Not met · 10 · evaluated, threshold not reached
PS2 No de novo observation with confirmed maternity and paternity has been identified for this variant. Details ▾Hide ▴
Evidence considered
- No de novo report identified in ClinVar
- literature
- or exploratory evidence retrieval
Still missing
- Targeted literature search for de novo reports of this variant in CADASIL or other NOTCH3-related disease may yield additional data
PM1 Pro1563 resides in EGF-like repeat 30 within the extracellular domain of NOTCH3, a region known to harbor CADASIL-causing mutations. However, established pathogenic NOTCH3 missense variants almost exclusively affect conserved cysteine residues within EGF repeats. Pro1563 is not a cysteine residue, and no evidence was identified to establish codon 1563 as a mutational hotspot or critical functional domain for which benign variation is absent. Details ▾Hide ▴
Evidence considered
- Pro1563 is located in EGF-like repeat 30
- but is not a cysteine residue
- Known pathogenic NOTCH3 missense variants predominantly affect cysteine residues in EGF repeats
Still missing
- No NOTCH3-specific PM1 domain definitions available from a CSPEC or VCEP
PM6 No de novo observation of this variant without confirmation of maternity and paternity was identified. Details ▾Hide ▴
Evidence considered
- No de novo report identified in any evidence source
Still missing
- A de novo observation even without parental confirmation could support PM6 if identified
PP2 NOTCH3 is not a gene with a low rate of benign missense variation. While missense variants are a common mechanism for CADASIL (particularly cysteine-altering substitutions in EGF repeats), the gene tolerates substantial missense variation in the general population and does not meet the PP2 requirement of having a low rate of benign missense variation. Details ▾Hide ▴
Evidence considered
- NOTCH3 harbors many missense variants in gnomAD at appreciable allele frequencies
- PP2 requires a gene with low benign missense variation rate
- which NOTCH3 does not exhibit overall
Sources
PP3 Multiple lines of computational evidence do not support a deleterious effect. REVEL score is 0.08 (below the 0.5 clinical threshold favoring pathogenicity). BayesDel score is -0.37 (below the 0.27 pathogenic threshold, consistent with a benign prediction). SpliceAI predicts no splicing impact (max delta = 0.00). Details ▾Hide ▴
Evidence considered
- REVEL score: 0.08 (benign-leaning
- below 0.5 threshold)
- BayesDel score: -0.37 (benign-leaning
- below 0.27 pathogenic threshold)
- SpliceAI max delta: 0.00 (no predicted splicing impact)
Sources
PP5 No reputable source (ClinVar, published literature) reports this variant as pathogenic with accessible evidence. The variant is absent from ClinVar, and OncoKB classifies it as 'Unknown Oncogenic Effect.' Details ▾Hide ▴
BA1 The variant has an allele frequency of 6.24e-7 in gnomAD v4.1 (1/1,602,340 alleles), far below the BA1 threshold of >1% (or >5% in some frameworks). Details ▾Hide ▴
BS1 The variant allele frequency (6.24e-7 in gnomAD v4.1; absent in v2.1) is far below the 0.3% threshold for BS1. CADASIL is a rare dominant disorder, and an allele frequency of this magnitude does not exceed what is expected for disease prevalence. Details ▾Hide ▴
Evidence considered
- gnomAD v4.1 AF = 0.0000624% (well below 0.3% BS1 threshold)
- gnomAD v2.1 AF = 0.0% (below BS1 threshold)
Sources
BP1 CADASIL is primarily caused by missense variants in NOTCH3, not exclusively by truncating variants. BP1 applies only when disease is caused exclusively by truncating variants in the gene. Details ▾Hide ▴
Evidence considered
- CADASIL is predominantly a missense-variant disorder (cysteine-altering substitutions in EGF repeats)
Sources
pvs1_gene_context4194730442147988411964313085450433860007
BP6 No reputable source reports this variant as benign. The variant is absent from ClinVar. Details ▾Hide ▴
Evidence considered
- Variant is absent from ClinVar
- no benign assertion available from any source
Sources
Not assessed · 9 · no assessment recorded
PS3 No well-established functional studies demonstrating a damaging effect for the exact variant NM_000435.2:c.4688C>T (p.Pro1563Leu) were identified. Details ▾Hide ▴
Evidence considered
- No functional assay data for this specific amino acid substitution were found in evidence brief
- exploratory retrieval
- or literature
Still missing
- Functional assays for NOTCH3 missense variants exist (Notch signaling reporters
- CADASIL models) but have not been published for Pro1563Leu
PS4 No case-control or cohort data demonstrating statistically significant enrichment of this variant in affected individuals versus controls were identified. Details ▾Hide ▴
Evidence considered
- No proband counts or case-control statistics available for this variant
Still missing
- No clinical cohort studies reporting this variant in CADASIL or other NOTCH3-related disease
PP1 No family cosegregation data were identified for this variant. Details ▾Hide ▴
Evidence considered
- No family studies or segregation reports for this variant were found
Still missing
- Family-based studies of CADASIL cohorts reporting this variant would be needed to assess PP1
PP4 No patient phenotype or family history data are available for this case. Details ▾Hide ▴
Evidence considered
- No patient clinical information provided for phenotype specificity assessment
Still missing
- Patient phenotype and family history would be required to assess PP4
BS2 A single allele is observed in gnomAD v4.1, but CADASIL has adult-onset with variable expressivity and the phenotype of the gnomAD individual is unknown. The ultra-low frequency (1/1,602,340) does not provide sufficient confidence that the individual is a healthy adult unaffected by a NOTCH3-related disorder. Details ▾Hide ▴
Evidence considered
- One allele in gnomAD v4.1 (1/1
- 602
- 340)
- phenotype of carrier unknown
- CADASIL has variable age of onset
- the gnomAD individual could be pre-symptomatic
Still missing
- Phenotype confirmation of the single gnomAD v4.1 carrier would be needed to apply BS2
Sources
BS3 No well-established functional studies demonstrating no damaging effect for the exact variant NM_000435.2:c.4688C>T were identified. Details ▾Hide ▴
Evidence considered
- No functional assay data demonstrating wild-type-like behavior for Pro1563Leu
Still missing
- Functional characterization of Pro1563Leu in Notch signaling or CADASIL models has not been published
BS4 No family segregation data (either positive or negative) were identified for this variant. Details ▾Hide ▴
Evidence considered
- No reports of non-segregation in affected families
Still missing
- Family studies showing lack of cosegregation with CADASIL would be required to apply BS4
BP2 No data on co-occurrence of this variant in trans with a known pathogenic NOTCH3 variant were identified. Details ▾Hide ▴
Evidence considered
- No observation of this variant in trans with a pathogenic NOTCH3 variant
Still missing
- Genotype phasing data or co-occurrence reports would be needed to assess BP2
BP5 No data are available on whether this variant has been observed in a case where an alternate molecular basis for disease has been identified. Details ▾Hide ▴
Evidence considered
- No case data available to assess alternative molecular etiology
Still missing
- Clinical information on the proband would be needed to assess if an alternate molecular cause is present
Not applicable · 5· recorded as not applicable Show reasons ▾Hide reasons ▴
PVS1 N/ANM_000435.2:c.4688C>T is a missense variant (p.Pro1563Leu), not a null variant (nonsense, frameshift, or canonical splice site). PVS1 is not applicable to missense variants in the generic ACMG/AMP framework (PMC6185798). Details ▾Hide ▴
Evidence considered
- Missense substitution at codon 1563 (Pro→Leu) does not fall into any PVS1 null-variant bucket
- Variant bucket classified as 'other' in PVS1 variant assessment
Sources
pvs1_variant_assessmentpvs1_generic_framework ↗
PS1 N/ANo evidence of another nucleotide change at c.4688 producing the same amino acid change (p.Pro1563Leu) that has been previously established as pathogenic. Details ▾Hide ▴
Evidence considered
- No ClinVar entry for this variant or any other variant at this codon changing Pro1563 to Leu
Sources
PM5 N/ANo known pathogenic missense variants at codon 1563 of NOTCH3 (i.e., different amino acid change at Pro1563) were identified to serve as PM5 comparators. The automated PM5 candidate collection found zero same-residue candidates. Details ▾Hide ▴
Evidence considered
- No pathogenic missense variants at Pro1563 identified in ClinVar or PM5 candidate search
Still missing
- Manual review of ClinVar and literature for any P/LP missense variants at NOTCH3 codon 1563 could be informative
Sources
pm5_candidatesclinvar ↗
BP7 N/ANM_000435.2:c.4688C>T is a missense variant (p.Pro1563Leu), not a synonymous/silent variant. BP7 applies only to silent variants with no predicted splice impact. Details ▾Hide ▴
PS5 N/APS5 is not a standard criterion in the ACMG/AMP 2015 generic framework. No applicable VCEP-specific PS5 definition exists for NOTCH3. Details ▾Hide ▴
Evidence considered
- No VCEP framework available for NOTCH3
- generic ACMG/AMP 2015 does not define a PS5 criterion
Sources
generic_acmg_combination_rules
Identifiers
- Gene
- NOTCH3
- Transcript
- NM_000435.2
- Coding (HGVS c.)
- NM_000435.2:c.4688C>T
- Protein (HGVS p.)
- NP_000426.2:p.(Pro1563Leu)
- GRCh38
- chr19:15174116 G>A
- GRCh37
- chr19:15284927 G>A
Gene diagram
Every interpreted variant in NOTCH3, mapped onto the exon structure of NM_000435.2. Select a row to find it on the plot.
NOTCH3NM_000435.2
Fetching transcript structure from UCSC…
Exons
—
Transcript span
—
Strand
—
Variants mapped
—
Source
UCSC ncbiRefSeqCurated
All variants in NOTCH3
—
Select a row to find it on the plot; use the link to open its page.
| Protein | Location | Classification | Link |
|---|
gnomAD v4.1
1 / 1,602,340 alleles
AF 6.24e-07 · 0 homozygotes
gnomAD v2.1
0 / 242,354 alleles
AF 0 · 0 homozygotes
gnomAD-Canada v1.0
0 / 0 alleles
AF 0 · 0 homozygotes · FAF 0
By genetic ancestry
gnomAD v4.1
AF 6.2e-07 · 1 / 1,602,340 alleles · 0 hom
| African/African American1 / 74,766 | 1.3e-05 |
0 alternate alleles recorded in 9 other groups: Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, European (non-Finnish).
gnomAD v2.1
AF 0 · 0 / 242,354 alleles · 0 hom
No alternate alleles recorded in the displayed ancestry groups.
gnomAD-Canada
AF 0 · 0 / 0 alleles · 0 hom
Statements
gnomAD v4.1
This variant is present in gnomAD v4.1 (AF= 6.24087e-07; MAF= 0.00006%, 1/1602340 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 1.33751e-05; MAF= 0.00134%, 1/74766 alleles, homozygotes = 0).
gnomAD v2.1
This variant is present in gnomAD v2.1 (AF= 0; MAF= 0.00000%, 0/242354 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 0; MAF= 0.00000%, 0/15004 alleles, homozygotes = 0).
SpliceAI and Pangolin
Other predictors
- REVEL
- 0.080
- BayesDel
- -0.371
How the predictions were used
BP4 SupportingMultiple lines of computational evidence support a benign impact. REVEL score is 0.08 (below 0.5 threshold), BayesDel score is -0.37 (below pathogenic threshold), and SpliceAI predicts no splicing impact (max delta = 0.00). All three in silico predictors are consistent with a benign or neutral effect. Details ▾Hide ▴
Evidence considered
- REVEL score: 0.08 (benign-leaning)
- BayesDel score: -0.37 (benign-leaning)
- SpliceAI max delta: 0.00 (no predicted splicing impact)
Sources
PP3 Multiple lines of computational evidence do not support a deleterious effect. REVEL score is 0.08 (below the 0.5 clinical threshold favoring pathogenicity). BayesDel score is -0.37 (below the 0.27 pathogenic threshold, consistent with a benign prediction). SpliceAI predicts no splicing impact (max delta = 0.00). Details ▾Hide ▴
Evidence considered
- REVEL score: 0.08 (benign-leaning
- below 0.5 threshold)
- BayesDel score: -0.37 (benign-leaning
- below 0.27 pathogenic threshold)
- SpliceAI max delta: 0.00 (no predicted splicing impact)
Sources
BP7 N/ANM_000435.2:c.4688C>T is a missense variant (p.Pro1563Leu), not a synonymous/silent variant. BP7 applies only to silent variants with no predicted splice impact. Details ▾Hide ▴
Statement
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.08. BayesDel score = -0.370843.
0 paper records listed. No publication is explicitly linked to an applied criterion in the recorded metadata.
Screenshots represent source records captured during evidence collection. Select one to view the recorded source content.
gnomAD v4.1
1 / 1,602,340 recorded alleles
Open source ↗
gnomAD v2.1
Captured gnomAD v2.1 source record
Open source ↗
SpliceAI Lookup
Recorded maximum delta 0.000
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_000435.2%3Ac.4688C%3ET
- gnomAD v2.1 ↗gnomad.broadinstitute.org/variant/19-15284927-G-A?dataset=gnomad_r2_1
- gnomAD v4.1 ↗gnomad.broadinstitute.org/variant/chr19-15174116-G-A?dataset=gn…
- SpliceAI Lookup ↗spliceailookup.broadinstitute.org/#variant=NM_000435.2%3Ac.4688…
- OncoKB ↗www.oncokb.org/gene/NOTCH3/P1563L
- COSMIC ↗cancer.sanger.ac.uk/cosmic/search?q=NOTCH3+c.4688C%3ET
- 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
This variant is present in gnomAD v4.1 (AF= 6.24087e-07; MAF= 0.00006%, 1/1602340 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 1.33751e-05; MAF= 0.00134%, 1/74766 alleles, homozygotes = 0).
gnomAD v2.1
This variant is present in gnomAD v2.1 (AF= 0; MAF= 0.00000%, 0/242354 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 0; MAF= 0.00000%, 0/15004 alleles, homozygotes = 0).
ClinVar
This variant is absent from ClinVar.
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.08. BayesDel score = -0.370843.
Functional
OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. NOTCH3 encodes a Type I transmembrane protein of the Notch family. Missense and nonsense mutations in NOTCH3 have been identified in various cancers.
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.