GPD1 p.Arg35=
c.105G>A · rs756545887 · VCV1607859
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0557%, eas)
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 1.3 | GERP -0.24, phastCons 1 |
| Overall | ||
| CADD | 9.102 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0557%
East Asian · 25/44,876 alleles
Filtering AF
0.0387%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.033%
Overall
0.00161%
26/1,612,186 alleles · ultra-rare
exomes 23/1,460,006 · genomes 3/152,180 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0557% | 1,795 |
| European (non-Finnish) | 8.49e-05% | 1,178,342 |
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
- GPD1
- Protein
- p.Arg35=
- Coding
- c.105G>A
- MANE Select
- NM_005276
- dbSNP
- rs756545887
- Type
- single nucleotide variant
- Location
- chr12:50104637 (GRCh38)
- Gene constraint
- LOEUF 0.891 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 96.39 · 7 PDB
- Residue 35
- a β-strand
Similar variants
- GPD1 p.Arg35Gln Uncertain significance ★★ ⚠ same residue
- GPD1 p.Arg229Gln Likely pathogenic ★★ same type
- GPD1 p.Ala202Val Uncertain significance ★★ ⚠ same type
- GPD1 p.Ala239Thr Uncertain significance ★★ ⚠ same type
- GPD1 p.Arg271Gln Uncertain significance ★★ ⚠ same type
- GPD1 p.Arg279His Uncertain significance ★★ ⚠ same type
- GPD1 p.Glu301Lys Uncertain significance ★★ ⚠ same type
- GPD1 p.Glu331Lys Uncertain significance ★★ ⚠ 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/gpd1-p-arg35 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown