HAP1 p.Thr503=
c.1509G>A · rs782272213 · VCV3038125
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00769%, sas)
Conditions
1
HAP1-related disorder
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 -0.2 |
| Overall | ||
| CADD | 5.041 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00769%
South Asian · 7/90,994 alleles
Filtering AF
0.00359%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00255%
Overall
0.00093%
15/1,612,348 alleles · very rare
exomes 14/1,460,198 · genomes 1/152,150 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00769% | 12,999 |
| East Asian | 0.00446% | 22,422 |
| European (non-Finnish) | 0.000509% | 196,506 |
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
- HAP1
- Protein
- p.Thr503=
- Coding
- c.1509G>A
- MANE Select
- NM_177977
- dbSNP
- rs782272213
- Type
- single nucleotide variant
- Location
- chr17:41725052 (GRCh38)
- Gene constraint
- LOEUF 1.31 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 64.28
Disease context
HAP1-related disorder
Similar variants
- HAP1 p.Thr503Met Uncertain significance ★ ⚠ same residue
- HAP1 c.1201-4C>T Likely benign same condition
- HAP1 c.1201-7C>T Likely benign same condition
- HAP1 c.470-7C>G Likely benign same condition
- HAP1 p.Ala21= Likely benign same condition
- HAP1 p.Ala505Val Benign same condition
- HAP1 p.Arg116Trp Likely benign same condition
- HAP1 p.Asp339Asn Likely benign 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/hap1-p-thr503 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown