Is GAPVD1 p.Pro854fs (c.2561del) pathogenic?

GAPVD1 p.Pro854fs (c.2561del) is classified Likely benign in GAPVD1 (ClinVar, Single submitter, 1 submitter; last evaluated 2020-11-19). No gnomAD frequency available for this variant; Associated with autism spectrum disorder.

What condition is associated with GAPVD1 p.Pro854fs (c.2561del)?

GAPVD1 p.Pro854fs (c.2561del) is associated with autism spectrum disorder (ClinVar).

How common is GAPVD1 p.Pro854fs (c.2561del) in the general population?

GAPVD1 p.Pro854fs (c.2561del) is no gnomAD frequency available for this variant (gnomAD).

GAPVD1 p.Pro854fs

c.2561del · rs2540820202 · VCV2429802

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

autism spectrum disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a LoF-intolerant gene
NMD	predicted	premature termination codon in exon 17 of 28
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 2.6	GERP -2, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. 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.Pro854fs
Coding: c.2561del
MANE Select: NM_001282680
dbSNP: rs2540820202
Type: Deletion
Location: chr9:125337274 (GRCh38)
Gene constraint: LOEUF 0.34 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 63.17
Residue 854: the 'disordered' region

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

Disease context

autism spectrum disorder — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

GAPVD1 c.3046+4del Uncertain significance ★ same type
GAPVD1 p.Leu612fs Uncertain significance ★ same type
GAPVD1 c.186-4_186-3del 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-pro854fs (accessed [today's date]).

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