HUNK p.Val513=
c.1539G>C · rs148050790 · VCV2652591
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.183%, mid)
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 7.9 | GERP 1.4, phastCons 1 |
| Overall | ||
| CADD | 12.27 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.183%
Middle Eastern · 11/6,018 alleles
Filtering AF
0.102%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0792%
Overall
0.0473%
762/1,610,022 alleles · rare
exomes 695/1,457,792 · genomes 67/152,230 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.183% | 547 |
| Admixed American | 0.0816% | 1,226 |
| European (non-Finnish) | 0.0532% | 1,880 |
| Remaining individualsnot grpmax-eligible | 0.045% | 2,224 |
| South Asian | 0.0431% | 2,323 |
| African / African-American | 0.00937% | 10,667 |
| Finnishnot grpmax-eligible | 0.00313% | 31,983 |
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
- HUNK
- Protein
- p.Val513=
- Coding
- c.1539G>C
- MANE Select
- NM_014586
- dbSNP
- rs148050790
- Type
- single nucleotide variant
- Location
- chr21:31998578 (GRCh38)
- Gene constraint
- LOEUF 0.39 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 62.83
Similar variants
- HUNK p.Ala272Ser Uncertain significance ★ ⚠ same type
- HUNK p.Ala4Val Uncertain significance ★ ⚠ same type
- HUNK p.Ala590Asp Uncertain significance ★ ⚠ same type
- HUNK p.Ala698Gly Uncertain significance ★ ⚠ same type
- HUNK p.Arg119His Uncertain significance ★ ⚠ same type
- HUNK p.Arg157Trp Uncertain significance ★ same type
- HUNK p.Arg164His Uncertain significance ★ ⚠ same type
- HUNK p.Arg179Trp 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/hunk-p-val513 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown