SRGAP1 p.Leu49=
c.145C>T · rs142409169 · VCV725157
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.16%, sas)
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 2.7 | GERP 2.5, phastCons 1 |
| Overall | ||
| CADD | 11.08 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.16%
South Asian · 137/85,706 alleles
Filtering AF
0.138%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.13%
Overall
0.0598%
944/1,577,814 alleles · rare
exomes 889/1,426,578 · genomes 55/151,236 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.16% | 626 |
| European (non-Finnish) | 0.0654% | 1,529 |
| Remaining individualsnot grpmax-eligible | 0.0512% | 1,953 |
| Middle Eastern | 0.0338% | 2,957 |
| African / African-American | 0.0149% | 6,711 |
| Admixed American | 0.0103% | 9,699 |
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.Leu49=
- Coding
- c.145C>T
- MANE Select
- NM_020762
- dbSNP
- rs142409169
- Type
- single nucleotide variant
- Location
- chr12:63984024 (GRCh38)
- Gene constraint
- LOEUF 0.47 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 73.49
- Residue 49
- the f-bar 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.Leu953Val Benign ★★ same type
- SRGAP1 p.Ser569Gly Likely 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-leu49 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown