SRCAP p.Pro63=
c.189C>G · rs79656879 · VCV160033
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 5 submitters
gnomAD v4.1
Common
common (popmax 7.21%, afr) — too common for a highly-penetrant pathogenic allele
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 -0.53 | GERP -4.7, phastCons 0.015 |
| Overall | ||
| CADD | 6.344 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
7.21%
African / African-American · 5,408/75,036 alleles
Filtering AF
7.05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 6.98%
Overall
0.583%
9,412/1,614,168 alleles · common
exomes 5,939/1,461,890 · genomes 3,473/152,278 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 7.21% | 14 |
| Ashkenazi Jewishnot grpmax-eligible | 3.47% | 29 |
| Remaining individualsnot grpmax-eligible | 0.846% | 118 |
| Admixed American | 0.71% | 141 |
| Middle Eastern | 0.61% | 164 |
| European (non-Finnish) | 0.16% | 626 |
| Finnishnot grpmax-eligible | 0.075% | 1,334 |
| South Asian | 0.0582% | 1,719 |
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.Pro63=
- Coding
- c.189C>G
- MANE Select
- NM_006662
- dbSNP
- rs79656879
- Type
- single nucleotide variant
- Location
- chr16:30704198 (GRCh38)
- Gene constraint
- LOEUF 0.223 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Residue 63
- the 'disordered' region
Similar variants
- SRCAP p.Pro63Leu 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
- SRCAP p.Gln2419Ter 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-pro63 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown