AP4M1 p.Arg362=
c.1086C>T · VCV4897061
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000339%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.147 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.31 | GERP 1.8 |
| Overall | ||
| CADD | 11.78 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000339%
European (non-Finnish) · 4/1,180,024 alleles
Filtering AF
7.9e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 5.4e-05%
Overall
0.000274%
4/1,461,562 alleles · very rare
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.Arg362=
- Coding
- c.1086C>T
- MANE Select
- NM_004722
- Type
- single nucleotide variant
- Location
- chr7:100106463 (GRCh38)
- Gene constraint
- LOEUF 1.106 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 86.16 · 6 PDB
- Residue 362
- the mhd domain; a β-strand
Similar variants
- AP4M1 p.Arg362Cys Uncertain significance ★ ⚠ same residue
- AP4M1 p.Arg362His Uncertain significance ★ ⚠ same residue
- AP4M1 c.1137+1G>T Pathogenic/Likely pathogenic ★★ same type
- AP4M1 c.930-1G>C Likely pathogenic ★★ same type
- AP4M1 p.Arg268Ter Pathogenic ★★ same type
- AP4M1 p.Arg306Ter Pathogenic ★★ same type
- AP4M1 p.Arg318Ter Pathogenic ★★ same type
- AP4M1 p.Arg338Ter Pathogenic/Likely 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-arg362 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown