Is AP1G1 p.Val336= (c.1008A>T) pathogenic?

AP1G1 p.Val336= (c.1008A>T) is classified Likely benign in AP1G1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-02-16). Absent from gnomAD v4.1.

How common is AP1G1 p.Val336= (c.1008A>T) in the general population?

AP1G1 p.Val336= (c.1008A>T) is absent from gnomAD v4.1 (gnomAD).

AP1G1 p.Val336=

c.1008A>T · VCV3911184

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

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 0.11	GERP -2.4, phastCons 0.92
Overall
CADD	7.412	PHRED · no single calibrated threshold — expert panels disagree

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: AP1G1
Protein: p.Val336=
Coding: c.1008A>T
MANE Select: NM_001128
Type: single nucleotide variant
Location: chr16:71758888 (GRCh38)
Gene constraint: LOEUF 0.113 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 84.56 · 1 PDB

Full AP1G1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

AP1G1 p.Val336Ile Likely benign ★ same residue
AP1G1 p.Arg15Trp Likely pathogenic ★★ same type
AP1G1 p.Arg416Ter Pathogenic ★★ same type
AP1G1 p.Arg46Ter Uncertain significance ★★ same type
AP1G1 p.Gly120Val Uncertain significance ★★ ⚠ same type
AP1G1 p.His575Asp Uncertain significance ★★ ⚠ same type
AP1G1 p.Ile769Val Uncertain significance ★★ ⚠ same type
AP1G1 c.2367+12A>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/ap1g1-p-val336 (accessed [today's date]).

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