IGSF10 p.Ser1925=
c.5775G>A · rs748385847 · VCV3012107
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0164%, 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 -20 | GERP -3.9 |
| Overall | ||
| CADD | 0.015 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0164%
Middle Eastern · 1/6,084 alleles
Filtering AF
0.000365%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000211%
Overall
0.00112%
18/1,614,092 alleles · ultra-rare
exomes 16/1,461,882 · genomes 2/152,210 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0164% | 6,084 |
| Remaining individualsnot grpmax-eligible | 0.0064% | 15,622 |
| East Asian | 0.00223% | 44,900 |
| South Asian | 0.0022% | 45,542 |
| Finnishnot grpmax-eligible | 0.00156% | 64,046 |
| African / African-American | 0.00133% | 74,926 |
| European (non-Finnish) | 0.000678% | 147,505 |
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.Ser1925=
- Coding
- c.5775G>A
- MANE Select
- NM_178822
- dbSNP
- rs748385847
- Type
- single nucleotide variant
- Location
- chr3:151443172 (GRCh38)
- Gene constraint
- LOEUF 1.068 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 58.70
- Residue 1925
- the ig-like c2-type 5 domain
Similar variants
- IGSF10 p.Ser1925Leu 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-ser1925 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown