SRGAP1 p.Ile930=
c.2790C>T · rs369231301 · VCV763910
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0183%, amr)
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 -20 | GERP -5.6 |
| Overall | ||
| CADD | 0.1 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0183%
Admixed American · 11/60,030 alleles
Filtering AF
0.0102%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00785%
Overall
0.00601%
97/1,614,118 alleles · ultra-rare
exomes 91/1,461,862 · genomes 6/152,256 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0183% | 5,457 |
| Remaining individualsnot grpmax-eligible | 0.008% | 12,502 |
| South Asian | 0.00769% | 13,010 |
| European (non-Finnish) | 0.00602% | 16,620 |
| African / African-American | 0.004% | 25,009 |
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.Ile930=
- Coding
- c.2790C>T
- MANE Select
- NM_020762
- dbSNP
- rs369231301
- Type
- single nucleotide variant
- Location
- chr12:64128110 (GRCh38)
- Gene constraint
- LOEUF 0.47 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 73.49
- Residue 930
- the 'disordered' region
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-ile930 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown