HDAC6 p.Val144=
c.432T>C · rs143689285 · VCV731665
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.97%, 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 1.3 | GERP 1.8, phastCons 1 |
| Overall | ||
| CADD | 8.593 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.97%
African / African-American · 1,106/56,078 alleles
Filtering AF
1.88%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.84%
Overall
0.109%
1,275/1,169,544 alleles · low-frequency
exomes 645/1,057,441 · genomes 630/112,103 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.97% | 51 |
| Remaining individualsnot grpmax-eligible | 0.173% | 577 |
| Admixed American | 0.122% | 823 |
| Middle Eastern | 0.116% | 861 |
| European (non-Finnish) | 0.00401% | 24,941 |
| South Asian | 0.00189% | 52,852 |
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
- HDAC6
- Protein
- p.Val144=
- Coding
- c.432T>C
- MANE Select
- NM_006044
- dbSNP
- rs143689285
- Type
- single nucleotide variant
- Location
- chrX:48805666 (GRCh38)
- Structure
- AlphaFold pLDDT 77.66 · 22 PDB
- Residue 144
- the 'histone deacetylase 1' region
Similar variants
- HDAC6 p.Ala374Gly Uncertain significance ★★ ⚠ same type
- HDAC6 c.1059+6G>C Likely benign ★★ same type
- HDAC6 c.2187+20G>A Benign ★★ same type
- HDAC6 p.Glu1017= Benign/Likely benign ★★ same type
- HDAC6 p.Glu889= Benign ★★ same type
- HDAC6 p.Gly1051= Benign/Likely benign ★★ same type
- HDAC6 p.Gly1083Asp Likely benign ★★ same type
- HDAC6 p.Gly930Arg 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/hdac6-p-val144 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown