Is GAPVD1 p.Arg477Ter (c.1429C>T) pathogenic?

GAPVD1 p.Arg477Ter (c.1429C>T) is classified Uncertain significance in GAPVD1 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2021-11-02). No allele count reported in gnomAD v4.1 (AN 1,603,366).

How common is GAPVD1 p.Arg477Ter (c.1429C>T) in the general population?

GAPVD1 p.Arg477Ter (c.1429C>T) is no allele count reported in gnomAD v4.1 (AN 1,603,366) (gnomAD).

GAPVD1 p.Arg477Ter

c.1429C>T · rs1177078143 · VCV1334636

Uncertain significance No assertion criteria

Classification

Uncertain significance

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

Consequence

nonsense (stop-gain)

predicted LoF

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,603,366)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	nonsense (stop-gain)	predicted loss-of-function in a LoF-intolerant gene
NMD	predicted	premature termination codon in exon 8 of 28
REVEL	0.222	benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 4.7	GERP 0.32, phastCons 1
Overall
CADD	37.0	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

No allele count reported in gnomAD v4.1 (AN 1,603,366). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: GAPVD1
Protein: p.Arg477Ter
Coding: c.1429C>T
MANE Select: NM_001282680
dbSNP: rs1177078143
Type: single nucleotide variant
Location: chr9:125307868 (GRCh38)
Gene constraint: LOEUF 0.34 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 63.17

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

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-arg477ter (accessed [today's date]).

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