NOTCH3 p.Arg1998=
c.5994T>G · rs1599360366 · VCV737858
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0531%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -3.2 | GERP -3.8 |
| Overall | ||
| CADD | 1.42 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0531%
European (non-Finnish) · 617/1,162,684 alleles
Filtering AF
0.0495%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0482%
Overall
0.0421%
671/1,594,428 alleles · ultra-rare
exomes 669/1,442,466 · genomes 2/151,962 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0531% | 1,884 |
| Remaining individualsnot grpmax-eligible | 0.0405% | 2,470 |
| Ashkenazi Jewishnot grpmax-eligible | 0.017% | 5,884 |
| South Asian | 0.0166% | 6,041 |
| Middle Eastern | 0.0165% | 6,046 |
| East Asian | 0.0067% | 14,923 |
| African / African-American | 0.00537% | 18,623 |
| Finnishnot grpmax-eligible | 0.00157% | 63,862 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- NOTCH3
- Protein
- p.Arg1998=
- Coding
- c.5994T>G
- MANE Select
- NM_000435
- dbSNP
- rs1599360366
- Type
- single nucleotide variant
- Location
- chr19:15161634 (GRCh38)
- Gene constraint
- LOEUF 0.566 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 61.79 · 6 PDB
- Residue 1998
- a UniProt-annotated variant site (in carasil1; likely pathogenic)
Similar variants
- NOTCH3 p.Arg1998Cys Conflicting classifications of pathogenicity ★ ⚠ same residue
- NOTCH3 p.Arg1998His Uncertain significance ★ ⚠ same residue
- NOTCH3 p.Arg1998fs Uncertain significance ★ same residue
- NOTCH3 c.341-2A>G Pathogenic ★★ same type
- NOTCH3 c.341-2A>T Pathogenic ★★ same type
- NOTCH3 p.Arg1006Cys Pathogenic ★★ ⚠ same type
- NOTCH3 p.Arg1076Cys Pathogenic/Likely pathogenic ★★ ⚠ same type
- NOTCH3 p.Arg110Cys Pathogenic ★★ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/notch3-p-arg1998 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown