Is GAPVD1 p.Val1376= (c.4128G>A) pathogenic?

GAPVD1 p.Val1376= (c.4128G>A) is classified Likely benign in GAPVD1 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2021-04-26). Very rare (popmax 0.00668%, eas); Associated with GAPVD1-related disorder.

What condition is associated with GAPVD1 p.Val1376= (c.4128G>A)?

GAPVD1 p.Val1376= (c.4128G>A) is associated with GAPVD1-related disorder (ClinVar).

How common is GAPVD1 p.Val1376= (c.4128G>A) in the general population?

GAPVD1 p.Val1376= (c.4128G>A) is very rare (popmax 0.00668%, eas) (gnomAD).

GAPVD1 p.Val1376=

c.4128G>A · rs754680831 · VCV3054761

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00668%, eas)

Conditions

GAPVD1-related disorder

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 0.6	GERP -1.8, phastCons 1
Overall
CADD	7.056	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00668% East Asian · 3/44,894 alleles

Filtering AF 0.00177% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000891%

Overall 0.0013% 21/1,613,706 alleles · very rare exomes 19/1,461,542 · genomes 2/152,164 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.00668%	14,965
European (non-Finnish)	0.00153%	65,540

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.Val1376=
Coding: c.4128G>A
MANE Select: NM_001282680
dbSNP: rs754680831
Type: single nucleotide variant
Location: chr9:125360611 (GRCh38)
Gene constraint: LOEUF 0.34 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 63.17
Residue 1376: the vps9 domain

Full GAPVD1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

GAPVD1-related disorder

Similar variants

GAPVD1 p.Arg1306Trp Uncertain significance ★ ⚠ same condition
GAPVD1 p.Arg487His Uncertain significance ★ ⚠ same condition
GAPVD1 p.Arg564His Uncertain significance ★ ⚠ same condition
GAPVD1 p.Ile1456Val Uncertain significance ★ ⚠ same condition
GAPVD1 p.Ser112Phe Uncertain significance ⚠ same condition
GAPVD1 c.1251+7G>A Likely benign same condition
GAPVD1 c.1441+17G>T Likely benign same condition
GAPVD1 c.1442-8T>C Likely benign 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/gapvd1-p-val1376 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown