INS p.Cys31=
c.93C>T · VCV4685869
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00534%, afr)
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 -4.2 | GERP -2.3 |
| Overall | ||
| CADD | 3.054 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00534%
African / African-American · 4/74,934 alleles
Filtering AF
0.002%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00176%
Overall
0.0026%
42/1,612,592 alleles · very rare
exomes 39/1,460,382 · genomes 3/152,210 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00534% | 18,734 |
| South Asian | 0.00329% | 30,363 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,221 |
| European (non-Finnish) | 0.0028% | 35,753 |
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
- INS
- Protein
- p.Cys31=
- Coding
- c.93C>T
- MANE Select
- NM_000207
- Type
- single nucleotide variant
- Location
- chr11:2160879 (GRCh38)
- Gene constraint
- LOEUF 1.195 · pLI 0.02 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 53.19 · 386 PDB
- Residue 31
- an α-helix; a disulfide bond
Similar variants
- INS p.Cys31Gly Uncertain significance ★ ⚠ same residue
- INS c.-152C>A Pathogenic/Likely pathogenic ★★ same type
- INS c.-152C>G Pathogenic ★★ same type
- INS p.Ala24Val Likely pathogenic ★★ ⚠ same type
- INS p.Arg89Cys Pathogenic/Likely pathogenic ★★ same type
- INS p.Arg89His Pathogenic/Likely pathogenic ★★ same type
- INS p.Gly32Ser Pathogenic/Likely pathogenic ★★ ⚠ same type
- INS p.Met1Val Pathogenic/Likely pathogenic ★★ 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/ins-p-cys31 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown