SRGAP1 p.Cys715=
c.2145C>T · VCV4589506
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0329%, mid)
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 -8.5 | GERP -5.2 |
| Overall | ||
| CADD | 0.133 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0329%
Middle Eastern · 2/6,070 alleles
Filtering AF
0.00581%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00242%
Overall
0.00248%
40/1,612,122 alleles · ultra-rare
exomes 38/1,459,990 · genomes 2/152,132 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0329% | 3,035 |
| East Asian | 0.0067% | 14,933 |
| African / African-American | 0.00535% | 18,707 |
| European (non-Finnish) | 0.00263% | 38,031 |
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.Cys715=
- Coding
- c.2145C>T
- MANE Select
- NM_020762
- Type
- single nucleotide variant
- Location
- chr12:64115814 (GRCh38)
- Gene constraint
- LOEUF 0.47 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 73.49
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-cys715 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown