SRCAP p.Pro2821=
c.8463C>T · rs377100819 · VCV2646410
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.224%, 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 -0.81 | GERP -4.1 |
| Overall | ||
| CADD | 0.59 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.224%
South Asian · 203/90,534 alleles
Filtering AF
0.199%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.189%
Overall
0.0148%
239/1,609,450 alleles · rare
exomes 228/1,457,186 · genomes 11/152,264 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.224% | 446 |
| Middle Eastern | 0.0497% | 2,011 |
| Remaining individualsnot grpmax-eligible | 0.016% | 6,231 |
| European (non-Finnish) | 0.00178% | 56,079 |
| Admixed American | 0.00169% | 59,194 |
| African / African-American | 0.00134% | 74,850 |
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.Pro2821=
- Coding
- c.8463C>T
- MANE Select
- NM_006662
- dbSNP
- rs377100819
- Type
- single nucleotide variant
- Location
- chr16:30738503 (GRCh38)
- Gene constraint
- LOEUF 0.223 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Residue 2821
- the 'disordered' region; a UniProt-annotated variant site (in dehmba); a UniProt-annotated variant site (in flhs)
Similar variants
- SRCAP p.Pro2821Ala Uncertain significance ★★ ⚠ same residue
- SRCAP p.Pro2821Leu Uncertain significance ★ ⚠ same residue
- 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
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-pro2821 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown