HCK p.Pro10=
c.30G>C · VCV4689749
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0336%, amr)
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 1.3 | GERP 1.2, phastCons 1 |
| Overall | ||
| CADD | 12.4 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0336%
Admixed American · 8/23,842 alleles
Filtering AF
0.0166%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0121%
Overall
0.00063%
8/1,269,268 alleles · ultra-rare
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
- HCK
- Protein
- p.Pro10=
- Coding
- c.30G>C
- MANE Select
- NM_002110
- Type
- single nucleotide variant
- Location
- chr20:32052454 (GRCh38)
- Gene constraint
- LOEUF 0.795 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 83.93 · 42 PDB
- Residue 10
- the 'disordered' region
Similar variants
- HCK p.Arg123Trp Uncertain significance ★★ ⚠ same type
- HCK p.Glu75Gln Uncertain significance ★★ ⚠ same type
- HCK p.Leu139Val Uncertain significance ★★ ⚠ same type
- HCK p.Ser5Pro Uncertain significance ★★ ⚠ same type
- HCK p.Ala44Thr Benign/Likely benign ★★ same type
- HCK p.Asn64= Benign ★★ same type
- HCK p.Asp231= Benign/Likely benign ★★ same type
- HCK p.Glu110= Likely 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/hck-p-pro10 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown