AHDC1 p.Ser58=
c.174C>T · rs759070023 · VCV1914739
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00552%, 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 -7.4 | GERP -2.9 |
| Overall | ||
| CADD | 1.25 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00552%
Admixed American · 3/54,380 alleles
Filtering AF
0.00169%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00145%
Overall
0.00234%
33/1,408,654 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00552% | 18,127 |
| European (non-Finnish) | 0.00243% | 41,130 |
| East Asian | 0.00226% | 44,174 |
| South Asian | 0.0012% | 83,546 |
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.Ser58=
- Coding
- c.174C>T
- MANE Select
- NM_001371928
- dbSNP
- rs759070023
- Type
- single nucleotide variant
- Location
- chr1:27551942 (GRCh38)
- Gene constraint
- LOEUF 0.168 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 38.82
- Residue 58
- the 'disordered' region
Similar variants
- AHDC1 p.Ser58Thr 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-ser58 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown