HID1 p.Pro156=
c.468G>A · VCV4872837
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.674%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.08 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -11 | GERP -2.5 |
| Overall | ||
| CADD | 3.724 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.674%
Admixed American · 404/59,974 alleles
Filtering AF
0.619%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.598%
Overall
0.0253%
409/1,613,554 alleles · rare
exomes 390/1,461,214 · genomes 19/152,340 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.674% | 148 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,466 |
| South Asian | 0.0011% | 91,012 |
| European (non-Finnish) | 0.000254% | 393,236 |
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
- HID1
- Protein
- p.Pro156=
- Coding
- c.468G>A
- MANE Select
- NM_030630
- Type
- single nucleotide variant
- Location
- chr17:74963001 (GRCh38)
- Gene constraint
- LOEUF 0.642 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 86.13
- Residue 156
- a UniProt-annotated variant site (in dee105; likely pathogenic)
Similar variants
- HID1 p.Asp201Asn Uncertain significance ★★ same type
- HID1 p.Ser87Leu Uncertain significance ★★ ⚠ same type
- DMC1 p.Met200Val Benign ★★ ⚠ same type
- HID1 c.1149+7C>T Benign ★★ same type
- HID1 p.Gln130Glu Benign ★★ same type
- HID1 p.His192Tyr Benign ★★ same type
- HID1 c.1149+1G>T Likely pathogenic ★ same type
- HID1 p.Arg668Ter Likely 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/hid1-p-pro156 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown