Is AP4M1 p.Arg367Trp (c.1099C>T) pathogenic?

AP4M1 p.Arg367Trp (c.1099C>T) is classified Uncertain significance in AP4M1 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2025-03-27). AlphaMissense: likely benign (0.2976); Very rare (popmax 0.004%, afr); Associated with Inborn genetic diseases.

What condition is associated with AP4M1 p.Arg367Trp (c.1099C>T)?

AP4M1 p.Arg367Trp (c.1099C>T) is associated with Inborn genetic diseases, hereditary spastic paraplegia 50 (ClinVar).

How common is AP4M1 p.Arg367Trp (c.1099C>T) in the general population?

AP4M1 p.Arg367Trp (c.1099C>T) is very rare (popmax 0.004%, afr) (gnomAD).

What do computational predictors say about AP4M1 p.Arg367Trp (c.1099C>T)?

AlphaMissense predicts likely benign (score 0.2976) — an in-silico prediction, not a clinical call.

AP4M1 p.Arg367Trp

c.1099C>T · rs569348805 · VCV1704896

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

AlphaMissense

likely benign

0.2976 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.004%, afr)

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.2976	likely benign
REVEL	0.32	indeterminate
SaProt	LLR -10.41	damaging
⇒ SaProt calls this damaging; AlphaMissense does not; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 4.9	GERP 1.8, phastCons 1
Regional constraint	o/e 1.07	unconstrained · MANE · 5,164 bp · p 0.093 · regional, not allelic
Overall
CADD	31.0	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.004% African / African-American · 3/75,036 alleles

Filtering AF 0.00106% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000539%

Overall 0.00124% 20/1,613,792 alleles · very rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.004%	25,012
Ashkenazi Jewishnot grpmax-eligible	0.00338%	29,608
South Asian	0.0022%	45,545
European (non-Finnish)	0.00119%	84,286

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: AP4M1
Protein: p.Arg367Trp
Coding: c.1099C>T
MANE Select: NM_004722
dbSNP: rs569348805
Type: single nucleotide variant
Location: chr7:100106476 (GRCh38)
Gene constraint: LOEUF 1.106 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 86.16 · 6 PDB
Residue 367: the mhd domain

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

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: hereditary spastic paraplegia 50

Similar variants

AP4M1 p.Arg367Gln Uncertain significance ★★ ⚠ same residue
AP4M1 c.1137+1G>T Pathogenic/Likely pathogenic ★★ same condition
AP4M1 c.930-1G>C Likely pathogenic ★★ same condition
AP4M1 p.Arg268Ter Pathogenic ★★ same condition
AP4M1 p.Arg306Ter Pathogenic ★★ same condition
AP4M1 p.Arg318Ter Pathogenic ★★ same condition
AP4M1 p.Arg338Ter Pathogenic/Likely pathogenic ★★ same condition
AP4M1 p.Cys319Arg Pathogenic/Likely pathogenic ★★ same condition

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-arg367trp (accessed [today's date]).

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