IGSF1 p.Pro767=
c.2301G>A · rs767364150 · VCV2661441
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0178%, eas)
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 1.5 | GERP 0.5, phastCons 1 |
| Overall | ||
| CADD | 6.834 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0178%
East Asian · 6/33,700 alleles
Filtering AF
0.00767%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00528%
Overall
0.00207%
25/1,206,839 alleles · ultra-rare
exomes 22/1,095,666 · genomes 3/111,173 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0178% | 5,617 |
| Admixed American | 0.00219% | 45,677 |
| Remaining individualsnot grpmax-eligible | 0.00211% | 47,449 |
| European (non-Finnish) | 0.0019% | 52,589 |
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
- IGSF1
- Protein
- p.Pro767=
- Coding
- c.2301G>A
- MANE Select
- NM_001555
- dbSNP
- rs767364150
- Type
- single nucleotide variant
- Location
- chrX:131277875 (GRCh38)
- Structure
- AlphaFold pLDDT 73.64
Similar variants
- IGSF1 p.Pro767Leu Likely benign ★ same residue
- IGSF1 p.Arg1184Ter Pathogenic ★★ same type
- IGSF1 p.Asp853Gly Uncertain significance ★★ ⚠ same type
- IGSF1 p.Ile1221Thr Uncertain significance ★★ ⚠ same type
- IGSF1 p.Thr1302Ile Uncertain significance ★★ ⚠ same type
- IGSF1 p.Thr1316Ile Uncertain significance ★★ ⚠ same type
- IGSF1 c.2041+24G>A Benign ★★ same type
- IGSF1 c.2042-70G>C 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/igsf1-p-pro767 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown