GAPVD1 p.Leu89=
c.265T>C · rs1401378608 · VCV1335738
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00223%, 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 0.14 | GERP -0.42, phastCons 0.014 |
| Overall | ||
| CADD | 7.335 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00223%
East Asian · 1/44,842 alleles
Overall
0.000186%
3/1,613,246 alleles · very rare
exomes 3/1,461,550 · genomes 0/151,696 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00223% | 44,842 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,488 |
| European (non-Finnish) | 8.48e-05% | 1,179,670 |
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
- GAPVD1
- Protein
- p.Leu89=
- Coding
- c.265T>C
- MANE Select
- NM_001282680
- dbSNP
- rs1401378608
- Type
- single nucleotide variant
- Location
- chr9:125302062 (GRCh38)
- Gene constraint
- LOEUF 0.34 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 63.17
Similar variants
- GAPVD1 c.1030-46T>C Benign ★★ same type
- GAPVD1 c.1251+51G>A Benign ★★ same type
- GAPVD1 c.1441+68G>C Benign ★★ same type
- GAPVD1 c.1733-44T>C Benign ★★ same type
- GAPVD1 c.1858+10A>G Benign ★★ same type
- GAPVD1 c.3410-96G>A Benign ★★ same type
- GAPVD1 c.3570-116A>G Benign ★★ same type
- GAPVD1 c.3972-107A>G Benign ★★ 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/gapvd1-p-leu89 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown