GPD2 p.Val484=
c.1452G>A · rs141790407 · VCV725226
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.397%, mid)
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 0.092 | GERP -3.4, phastCons 0.93 |
| Overall | ||
| CADD | 5.318 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.397%
Middle Eastern · 24/6,050 alleles
Filtering AF
0.273%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.233%
Overall
0.0253%
408/1,613,138 alleles · rare
exomes 382/1,460,992 · genomes 26/152,146 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.397% | 252 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0981% | 1,019 |
| South Asian | 0.0933% | 1,072 |
| Remaining individualsnot grpmax-eligible | 0.0464% | 2,154 |
| Admixed American | 0.0434% | 2,306 |
| European (non-Finnish) | 0.0181% | 5,537 |
| African / African-American | 0.00267% | 37,473 |
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
- GPD2
- Protein
- p.Val484=
- Coding
- c.1452G>A
- MANE Select
- NM_000408
- dbSNP
- rs141790407
- Type
- single nucleotide variant
- Location
- chr2:156569514 (GRCh38)
- Gene constraint
- LOEUF 0.796 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 86.47
Similar variants
- GPD2 p.Asn224Lys Uncertain significance ★★ ⚠ same type
- GPD2 p.Ile308Val Likely benign ★★ same type
- GPD2 c.497+5G>A Uncertain significance ★ same type
- GPD2 p.Ala233Pro Uncertain significance ★ ⚠ same type
- GPD2 p.Ala305Thr Uncertain significance ★ ⚠ same type
- GPD2 p.Ala499Thr Conflicting classifications of pathogenicity ★ ⚠ same type
- GPD2 p.Ala512Ser Uncertain significance ★ ⚠ same type
- GPD2 p.Ala565Ser 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/gpd2-p-val484 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown