SRGAP1 p.Phe511=
c.1533C>T · rs1049114341 · VCV764852
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00225%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 6 | GERP 2.8, phastCons 1 |
| Overall | ||
| CADD | 15.29 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00225%
South Asian · 2/89,004 alleles
Filtering AF
0.00123%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00105%
Overall
0.00156%
25/1,603,552 alleles · very rare
exomes 21/1,451,426 · genomes 4/152,126 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00225% | 44,502 |
| European (non-Finnish) | 0.00187% | 53,345 |
| African / African-American | 0.00134% | 74,710 |
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
- SRGAP1
- Protein
- p.Phe511=
- Coding
- c.1533C>T
- MANE Select
- NM_020762
- dbSNP
- rs1049114341
- Type
- single nucleotide variant
- Location
- chr12:64091372 (GRCh38)
- Gene constraint
- LOEUF 0.47 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 73.49
- Residue 511
- the rho-gap domain
Similar variants
- SRGAP1 p.Arg900Gly Uncertain significance ★★ ⚠ same type
- SRGAP1 c.2225-7G>A Likely benign ★★ same type
- SRGAP1 p.Asn786= Benign ★★ same type
- SRGAP1 p.His875Arg Benign ★★ same type
- SRGAP1 p.His924= Benign ★★ same type
- SRGAP1 p.Ile371= Benign ★★ same type
- SRGAP1 p.Leu49= Benign/Likely benign ★★ same type
- SRGAP1 p.Leu953Val Benign ★★ 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/srgap1-p-phe511 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown