SRCAP p.Arg898=
c.2694A>G · rs574210456 · VCV2428120
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.158%, sas)
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 0.88 | GERP -5.4, phastCons 0.99 |
| Overall | ||
| CADD | 6.993 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.158%
South Asian · 144/91,084 alleles
Filtering AF
0.137%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.129%
Overall
0.00973%
157/1,614,172 alleles · rare
exomes 146/1,461,894 · genomes 11/152,278 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.158% | 633 |
| Middle Eastern | 0.033% | 3,031 |
| Admixed American | 0.00833% | 12,005 |
| Remaining individualsnot grpmax-eligible | 0.008% | 12,501 |
| European (non-Finnish) | 8.47e-05% | 1,180,022 |
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
- SRCAP
- Protein
- p.Arg898=
- Coding
- c.2694A>G
- MANE Select
- NM_006662
- dbSNP
- rs574210456
- Type
- single nucleotide variant
- Location
- chr16:30716356 (GRCh38)
- Gene constraint
- LOEUF 0.223 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Residue 898
- an α-helix; a UniProt-annotated variant site (in dehmba)
Similar variants
- SRCAP p.Arg2329Ter Pathogenic/Likely pathogenic ★★ same type
- SRCAP p.Arg2435Ter Pathogenic/Likely pathogenic ★★ same type
- SRCAP p.Arg2444Ter Pathogenic ★★ same type
- SRCAP p.Arg2718Ter Pathogenic/Likely pathogenic ★★ same type
- SRCAP p.Arg2748Ter Pathogenic ★★ same type
- SRCAP p.Gln2407Ter Pathogenic ★★ same type
- SRCAP p.Gln2419Ter Pathogenic ★★ same type
- SRCAP p.Gln2665Ter Pathogenic/Likely 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/srcap-p-arg898 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown