AHDC1 p.Phe981=
c.2943C>T · rs555542437 · VCV1237031
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.259%, 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 -3.2 | GERP -4.1 |
| Overall | ||
| CADD | 0.177 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.259%
South Asian · 224/86,346 alleles
Filtering AF
0.232%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.221%
Overall
0.0181%
285/1,578,096 alleles · rare
exomes 273/1,425,730 · genomes 12/152,366 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.259% | 385 |
| Remaining individualsnot grpmax-eligible | 0.0229% | 4,358 |
| Middle Eastern | 0.0169% | 5,926 |
| East Asian | 0.00674% | 14,831 |
| African / African-American | 0.00537% | 18,631 |
| Admixed American | 0.00344% | 29,029 |
| European (non-Finnish) | 0.00319% | 31,391 |
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.Phe981=
- Coding
- c.2943C>T
- MANE Select
- NM_001371928
- dbSNP
- rs555542437
- Type
- single nucleotide variant
- Location
- chr1:27549173 (GRCh38)
- Gene constraint
- LOEUF 0.168 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 38.82
- Residue 981
- a UniProt-annotated variant site (in xigis); a UniProt-annotated variant site (in xigis; impaired nuclear localization); a UniProt-annotated variant site (in xigis; does not affect nuclear localization)
Similar variants
- AHDC1 p.Phe981Leu Uncertain significance ⚠ 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-phe981 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown