SRCAP p.Pro1400del
c.4196CTC[1] · rs530668607 · VCV2068610
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0714%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 2.6 | GERP 2.5, phastCons 1 |
| Overall | ||
| CADD | 14.24 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0714%
South Asian · 65/91,034 alleles
Filtering AF
0.0574%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0524%
Overall
0.0115%
186/1,613,350 alleles · ultra-rare
exomes 178/1,461,614 · genomes 8/151,736 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0714% | 1,401 |
| Remaining individualsnot grpmax-eligible | 0.0272% | 3,674 |
| East Asian | 0.0178% | 5,608 |
| European (non-Finnish) | 0.00771% | 12,964 |
| African / African-American | 0.00401% | 24,915 |
| Admixed American | 0.00334% | 29,974 |
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.Pro1400del
- Coding
- c.4196CTC[1]
- MANE Select
- NM_006662
- dbSNP
- rs530668607
- Type
- Microsatellite
- Location
- chr16:30723620 (GRCh38)
- Gene constraint
- LOEUF 0.223 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Residue 1400
- a UniProt-annotated variant site (in dehmba)
Similar variants
- SRCAP p.Pro1400Arg Uncertain significance ★ same residue
- SRCAP p.Pro1400= Likely benign ★ same residue
- SRCAP p.Gln2770del Uncertain significance ★★ same type
- SRCAP p.Glu3182del Uncertain significance ★★ same type
- SRCAP p.Pro2488del Uncertain significance ★★ same type
- SRCAP p.Ser2576del Uncertain significance ★★ same type
- SRCAP p.2992TVT[1] Benign/Likely benign ★★ same type
- SRCAP p.Glu180fs 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-pro1400del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown