GRHPR p.Ala17=
c.51C>T · rs138843824 · VCV1154506
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00937%, 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 -4.4 | GERP -3.4 |
| Overall | ||
| CADD | 9.198 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00937%
African / African-American · 7/74,744 alleles
Filtering AF
0.00438%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00309%
Overall
0.000437%
7/1,602,692 alleles · very rare
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
- GRHPR
- Protein
- p.Ala17=
- Coding
- c.51C>T
- MANE Select
- NM_012203
- dbSNP
- rs138843824
- Type
- single nucleotide variant
- Location
- chr9:37422801 (GRCh38)
- Gene constraint
- LOEUF 1.313 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 96.80 · 4 PDB
- Residue 17
- an α-helix
Similar variants
- GRHPR p.Ala17Gly Uncertain significance ★ ⚠ same residue
- GRHPR p.Ala17Val Uncertain significance ⚠ same residue
- GRHPR p.Ala17fs Pathogenic same residue
- GRHPR c.404+5G>A Likely pathogenic ★★ same type
- GRHPR c.493+2T>A Pathogenic/Likely pathogenic ★★ same type
- GRHPR c.494-2A>G Pathogenic/Likely pathogenic ★★ same type
- GRHPR c.734+1G>A Pathogenic/Likely pathogenic ★★ same type
- GRHPR c.735-1G>A Pathogenic/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/grhpr-p-ala17 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown