HID1 p.Pro693=
c.2079G>T · VCV4936971
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.264%, afr)
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 -20 | GERP -2.6 |
| Overall | ||
| CADD | 0.027 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.264%
African / African-American · 198/75,040 alleles
Filtering AF
0.234%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.222%
Overall
0.0292%
472/1,613,860 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.264% | 379 |
| Middle Eastern | 0.099% | 1,010 |
| Admixed American | 0.0933% | 1,072 |
| Remaining individualsnot grpmax-eligible | 0.0496% | 2,016 |
| European (non-Finnish) | 0.0144% | 6,941 |
| South Asian | 0.0121% | 8,280 |
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.Pro693=
- Coding
- c.2079G>T
- MANE Select
- NM_030630
- Type
- single nucleotide variant
- Location
- chr17:74952334 (GRCh38)
- Gene constraint
- LOEUF 0.642 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 86.13
- Residue 693
- a UniProt-annotated variant site (in dee105; likely pathogenic); the 'required for protein function' region
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-pro693 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown