IGSF1 p.Ser819=
c.2457C>A · VCV4471485
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00297%, 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 1.6 | GERP -1.1, phastCons 1 |
| Overall | ||
| CADD | 7.009 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00297%
East Asian · 1/33,722 alleles
Overall
8.27e-05%
1/1,209,527 alleles · very rare
exomes 0/1,097,980 · genomes 1/111,547 · joint denominator
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.Ser819=
- Coding
- c.2457C>A
- MANE Select
- NM_001555
- Type
- single nucleotide variant
- Location
- chrX:131277090 (GRCh38)
- Structure
- AlphaFold pLDDT 73.64
- Residue 819
- the ig-like c2-type 8 domain
Similar variants
- 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
- IGSF1 c.2896+34G>A 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-ser819 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown