IGSF10 p.Pro2367=
c.7101T>G · rs16863390 · VCV1601101
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 9.93%, eas) — too common for a highly-penetrant pathogenic allele
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 -0.98 | GERP -4.5 |
| Overall | ||
| CADD | 2.072 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
9.93%
East Asian · 4,458/44,882 alleles
Filtering AF
9.69%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 9.59%
Overall
2.66%
43,014/1,614,160 alleles · common
exomes 39,298/1,461,844 · genomes 3,716/152,316 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 9.93% | 10 |
| Finnishnot grpmax-eligible | 6.22% | 16 |
| South Asian | 4.4% | 23 |
| Admixed American | 2.77% | 36 |
| Remaining individualsnot grpmax-eligible | 2.68% | 37 |
| European (non-Finnish) | 2.24% | 45 |
| Ashkenazi Jewishnot grpmax-eligible | 1.34% | 75 |
| Middle Eastern | 1.29% | 78 |
| African / African-American | 0.405% | 247 |
| Amishnot grpmax-eligible | 0.219% | 456 |
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
- IGSF10
- Protein
- p.Pro2367=
- Coding
- c.7101T>G
- MANE Select
- NM_178822
- dbSNP
- rs16863390
- Type
- single nucleotide variant
- Location
- chr3:151437460 (GRCh38)
- Gene constraint
- LOEUF 1.068 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 58.70
- Residue 2367
- the ig-like c2-type 10 domain
Similar variants
- IGSF10 p.Pro2367Thr Uncertain significance ★ ⚠ same residue
- IGSF10 p.Ala1666Gly Uncertain significance ★★ ⚠ same type
- IGSF10 p.Ala1725Thr Uncertain significance ★★ ⚠ same type
- IGSF10 p.Ala275Thr Uncertain significance ★★ ⚠ same type
- IGSF10 p.Arg1484Thr Uncertain significance ★★ ⚠ same type
- IGSF10 p.Arg1684Thr Uncertain significance ★★ ⚠ same type
- IGSF10 p.Arg2403Gln Uncertain significance ★★ ⚠ same type
- IGSF10 p.Arg2410His Uncertain significance ★★ ⚠ 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/igsf10-p-pro2367 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown