Is AP4M1 p.Phe77fs (c.228_231del) pathogenic?

AP4M1 p.Phe77fs (c.228231del) is classified Pathogenic in AP4M1 (ClinVar, Single submitter, 1 submitter; last evaluated 2019-10-01). Absent from gnomAD.

How common is AP4M1 p.Phe77fs (c.228_231del) in the general population?

AP4M1 p.Phe77fs (c.228_231del) is absent from gnomAD (gnomAD).

AP4M1 p.Phe77fs

c.228_231del · rs2116628120 · VCV1701528

Pathogenic Single submitter

Classification

Pathogenic

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
NMD	predicted	premature termination codon in exon 3 of 15
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7.6	GERP 2.1, 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: AP4M1
Protein: p.Phe77fs
Coding: c.228_231del
MANE Select: NM_004722
dbSNP: rs2116628120
Type: Deletion
Location: chr7:100102754 (GRCh38)
Gene constraint: LOEUF 1.106 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 86.16 · 6 PDB

Full AP4M1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

AP4M1 p.Leu377fs Pathogenic/Likely pathogenic ★★ same type
AP4M1 p.Lys11fs Pathogenic/Likely pathogenic ★★ same type
AP4M1 p.Val48fs Pathogenic/Likely pathogenic ★★ same type
AP4M1 c.52_58+6del Pathogenic ★ same type
AP4M1 c.58+1_58+2del Likely pathogenic ★ same type
AP4M1 c.607-2_607-1del Likely pathogenic ★ same type
AP4M1 p.Ala87fs Likely pathogenic ★ same type
AP4M1 p.Arg338fs Pathogenic ★ 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/ap4m1-p-phe77fs (accessed [today's date]).

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