AHDC1 p.Pro100=
c.300G>A · rs148116899 · VCV3013841
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00667%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -5.2 | GERP -3.4 |
| Overall | ||
| CADD | 3.452 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00667%
Admixed American · 4/59,980 alleles
Filtering AF
0.00226%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00135%
Overall
0.00161%
26/1,611,946 alleles · very rare
exomes 23/1,459,990 · genomes 3/151,956 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00667% | 14,995 |
| African / African-American | 0.00401% | 24,933 |
| South Asian | 0.0022% | 45,527 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,440 |
| Finnishnot grpmax-eligible | 0.0016% | 62,466 |
| European (non-Finnish) | 0.00127% | 78,655 |
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.Pro100=
- Coding
- c.300G>A
- MANE Select
- NM_001371928
- dbSNP
- rs148116899
- Type
- single nucleotide variant
- Location
- chr1:27551816 (GRCh38)
- Gene constraint
- LOEUF 0.168 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 38.82
- Residue 100
- the 'disordered' region
Similar variants
- AHDC1 p.Pro100Leu 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-pro100 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown