MINK1 p.Pro650=
c.1950C>G · rs201027643 · VCV2647273
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.79%, sas)
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 -3 |
| Overall | ||
| CADD | 6.359 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.79%
South Asian · 702/88,836 alleles
Filtering AF
0.742%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.722%
Overall
0.048%
769/1,600,584 alleles · rare
exomes 745/1,448,238 · genomes 24/152,346 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.79% | 127 |
| Remaining individualsnot grpmax-eligible | 0.0484% | 2,068 |
| Middle Eastern | 0.0331% | 3,023 |
| Admixed American | 0.00521% | 19,185 |
| European (non-Finnish) | 0.00255% | 39,147 |
| Finnishnot grpmax-eligible | 0.0016% | 62,450 |
| African / African-American | 0.00134% | 74,808 |
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
- MINK1
- Protein
- p.Pro650=
- Coding
- c.1950C>G
- MANE Select
- NM_153827
- dbSNP
- rs201027643
- Type
- single nucleotide variant
- Location
- chr17:4891665 (GRCh38)
- Gene constraint
- LOEUF 0.403 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 64.32 · 1 PDB
- Residue 650
- the 'disordered' region
Similar variants
- CHRNE c.*745G>A Benign ★★ same type
- MINK1 p.Ile705Leu Benign/Likely benign ★★ same type
- CHRNE c.*806G>A Uncertain significance ★ same type
- CHRNE c.*876G>A Uncertain significance ★ same type
- MINK1 c.2199-2A>G Uncertain significance ★ same type
- MINK1 c.2401-149G>A Uncertain significance ★ same type
- MINK1 p.Ala445Val Uncertain significance ★ ⚠ same type
- MINK1 p.Ala632Thr 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/mink1-p-pro650 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown