AHDC1 p.Arg403=
c.1209C>T · rs113173951 · VCV1169789
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 6 submitters
gnomAD v4.1
Common
common (popmax 10.3%, mid) — too common for a highly-penetrant pathogenic allele
Conditions
1
AHDC1-related intellectual disability - obstructive sleep apnea - mild dysmorphism syndrome
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 0.29 | GERP -1.8, phastCons 0.9 |
| Overall | ||
| CADD | 7.25 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
10.3%
Middle Eastern · 620/6,042 alleles
Filtering AF
9.59%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 9.33%
Overall
8.03%
128,191/1,595,450 alleles · common
exomes 115,621/1,443,174 · genomes 12,570/152,276 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 10.3% | 10 |
| African / African-American | 9.24% | 11 |
| Amishnot grpmax-eligible | 8.9% | 11 |
| European (non-Finnish) | 8.73% | 11 |
| Remaining individualsnot grpmax-eligible | 7.72% | 13 |
| Finnishnot grpmax-eligible | 7.64% | 13 |
| Ashkenazi Jewishnot grpmax-eligible | 7.16% | 14 |
| Admixed American | 4.96% | 20 |
| South Asian | 4.01% | 25 |
| East Asian | 0.892% | 112 |
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.Arg403=
- Coding
- c.1209C>T
- MANE Select
- NM_001371928
- dbSNP
- rs113173951
- Type
- single nucleotide variant
- Location
- chr1:27550907 (GRCh38)
- Gene constraint
- LOEUF 0.168 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 38.82
- Residue 403
- a DNA-binding region; a UniProt-annotated variant site (in xigis); a UniProt-annotated variant site (in xigis; impaired nuclear localization); the 'disordered' region
Similar variants
- AHDC1 p.Arg403His Likely benign ★★ same residue
- AHDC1 p.Arg403Cys Uncertain significance ★ ⚠ same residue
- AHDC1 p.Arg1272Ter Pathogenic ★★ same condition
- AHDC1 p.Arg151Ter Pathogenic/Likely pathogenic ★★ same condition
- AHDC1 p.Arg587Ter Pathogenic ★★ same condition
- AHDC1 p.Arg688Ter Pathogenic ★★ same condition
- AHDC1 p.Arg789Ter Pathogenic ★★ same condition
- AHDC1 p.Arg925Ter Pathogenic/Likely pathogenic ★★ same condition
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-arg403 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown