HDAC6 p.Ser190=
c.570T>A · rs149790381 · VCV753679
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.083%, 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 -2.2 | GERP -3.9 |
| Overall | ||
| CADD | 5.728 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.083%
Admixed American · 38/45,810 alleles
Filtering AF
0.0621%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0549%
Overall
0.00323%
39/1,208,601 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.083% | 1,206 |
| European (non-Finnish) | 0.000112% | 893,767 |
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.Ser190=
- Coding
- c.570T>A
- MANE Select
- NM_006044
- dbSNP
- rs149790381
- Type
- single nucleotide variant
- Location
- chrX:48806644 (GRCh38)
- Structure
- AlphaFold pLDDT 77.66 · 22 PDB
- Residue 190
- 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-ser190 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown