HDAC7 p.Thr243=
c.729G>A · rs148220732 · VCV784299
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.688%, 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 -9.4 | GERP -3.1 |
| Overall | ||
| CADD | 2.193 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.688%
Middle Eastern · 41/5,962 alleles
Filtering AF
0.521%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.463%
Overall
0.156%
2,498/1,597,226 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.688% | 145 |
| Ashkenazi Jewishnot grpmax-eligible | 0.415% | 241 |
| Admixed American | 0.39% | 256 |
| Remaining individualsnot grpmax-eligible | 0.225% | 444 |
| European (non-Finnish) | 0.165% | 607 |
| African / African-American | 0.0554% | 1,804 |
| South Asian | 0.00686% | 14,580 |
| East Asian | 0.00447% | 22,352 |
| Finnishnot grpmax-eligible | 0.00157% | 63,792 |
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
- HDAC7
- Protein
- p.Thr243=
- Coding
- c.729G>A
- MANE Select
- NM_015401
- dbSNP
- rs148220732
- Type
- single nucleotide variant
- Location
- chr12:47796273 (GRCh38)
- Gene constraint
- LOEUF 0.344 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 62.90 · 6 PDB
- Residue 243
- the 'transcription repression 1' region; the 'transcription repression 2' region
Similar variants
- HDAC7 p.Thr243Met Uncertain significance ★ ⚠ same residue
- HDAC7 p.Arg201= Benign/Likely benign ★★ same type
- HDAC7 p.Leu233= Benign/Likely benign ★★ same type
- HDAC7 p.Ala138Val Uncertain significance ★ ⚠ same type
- HDAC7 p.Ala266Val Uncertain significance ★ ⚠ same type
- HDAC7 p.Ala337Gly Uncertain significance ★ ⚠ same type
- HDAC7 p.Ala337Thr Uncertain significance ★ ⚠ same type
- HDAC7 p.Ala431Gly 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/hdac7-p-thr243 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown