Is AP1G1 p.Pro675fs (c.2024del) pathogenic?

AP1G1 p.Pro675fs (c.2024del) is classified Uncertain significance in AP1G1 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-02-01). No gnomAD frequency available for this variant.

How common is AP1G1 p.Pro675fs (c.2024del) in the general population?

AP1G1 p.Pro675fs (c.2024del) is no gnomAD frequency available for this variant (gnomAD).

AP1G1 p.Pro675fs

c.2024del · rs2543500689 · VCV3253546

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

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 20 of 23
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 0.66	GERP 0.98, phastCons 0.95

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: AP1G1
Protein: p.Pro675fs
Coding: c.2024del
MANE Select: NM_001128
dbSNP: rs2543500689
Type: Deletion
Location: chr16:71739317 (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.Gln680fs Likely pathogenic ★ same type
AP1G1 p.Met26fs Pathogenic ★ same type
AP1G1 p.Tyr290fs Likely pathogenic ★ same type
AP1G1 p.Tyr432fs Pathogenic ★ same type
AP1G1 p.Glu30fs Uncertain significance ★ same type
AP1G1 p.Ile530_Ser534del Uncertain significance ★ same type
AP1G1 p.Lys410_Tyr411insTer Uncertain significance ★ same type
AP1G1 p.Val293_Leu294insTer Uncertain significance ★ 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-pro675fs (accessed [today's date]).

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