AHDC1 p.Val712=
c.2136C>T · rs559351156 · VCV1896402
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0431%, sas)
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 -6.5 | GERP -3.8 |
| Overall | ||
| CADD | 0.024 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0431%
South Asian · 39/90,458 alleles
Filtering AF
0.0324%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0286%
Overall
0.00324%
52/1,603,368 alleles · ultra-rare
exomes 48/1,451,298 · genomes 4/152,070 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0431% | 2,319 |
| East Asian | 0.0112% | 8,926 |
| Remaining individualsnot grpmax-eligible | 0.00162% | 61,870 |
| European (non-Finnish) | 0.000596% | 167,653 |
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
- AHDC1
- Protein
- p.Val712=
- Coding
- c.2136C>T
- MANE Select
- NM_001371928
- dbSNP
- rs559351156
- Type
- single nucleotide variant
- Location
- chr1:27549980 (GRCh38)
- Gene constraint
- LOEUF 0.168 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 38.82
- Residue 712
- a UniProt-annotated variant site (in xigis); a UniProt-annotated variant site (in xigis; impaired nuclear localization)
Similar variants
- AHDC1 p.Val712Gly Likely benign same residue
- AHDC1 p.Arg1272Ter Pathogenic ★★ same type
- AHDC1 p.Arg151Ter Pathogenic/Likely pathogenic ★★ same type
- AHDC1 p.Arg587Ter Pathogenic ★★ same type
- AHDC1 p.Arg688Ter Pathogenic ★★ same type
- AHDC1 p.Arg789Ter Pathogenic ★★ same type
- AHDC1 p.Arg925Ter Pathogenic/Likely pathogenic ★★ same type
- AHDC1 p.Gln332Ter Pathogenic ★★ 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/ahdc1-p-val712 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown