GPD1 p.Trp14Ter
c.42G>A · VCV4265533
Likely pathogenic
Single submitter
Classification
Likely pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
nonsense (stop-gain)
predicted LoF
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
Inborn genetic diseases
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Consequence | nonsense (stop-gain) | predicted loss-of-function |
|---|---|---|
| NMD | predicted | premature termination codon in exon 2 of 8 |
| Splicing | ||
| SpliceAI | Δ0.20 | acceptor gain · deltas |
| Constraint at this position | ||
| Conservation | phyloP 12 | GERP 1.9, phastCons 1 |
| Overall | ||
| CADD | 45.0 | PHRED · no single calibrated threshold — expert panels disagree |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- GPD1
- Protein
- p.Trp14Ter
- Coding
- c.42G>A
- MANE Select
- NM_005276
- Type
- single nucleotide variant
- Location
- chr12:50104574 (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 14
- a binding site; an α-helix
Similar variants
- GPD1 p.Trp14Arg Uncertain significance ★ ⚠ same residue
- GPD1 p.Ala202Val Uncertain significance ★★ ⚠ same condition
- GPD1 p.Arg271Gln Uncertain significance ★★ ⚠ same condition
- GPD1 p.Arg35Gln Uncertain significance ★★ ⚠ same condition
- GPD1 p.Glu301Lys Uncertain significance ★★ ⚠ same condition
- GPD1 p.Glu331Lys Uncertain significance ★★ ⚠ same condition
- GPD1 p.Gly267Arg Uncertain significance ★★ ⚠ same condition
- GPD1 p.Lys240Gln Uncertain significance ★★ ⚠ same condition
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-trp14ter (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown