AP4M1 p.Leu393=
c.1179C>T · rs2546963641 · VCV2583051
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Not reported
no allele count reported in gnomAD v4.1 (AN 1,613,680)
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 -1.4 | GERP -3.5 |
| Overall | ||
| CADD | 0.62 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
No allele count reported in gnomAD v4.1 (AN 1,613,680). 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.Leu393=
- Coding
- c.1179C>T
- MANE Select
- NM_004722
- dbSNP
- rs2546963641
- Type
- single nucleotide variant
- Location
- chr7:100106699 (GRCh38)
- Gene constraint
- LOEUF 1.106 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 86.16 · 6 PDB
- Residue 393
- the mhd domain
Similar variants
- 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
- AP4M1 p.Cys319Arg Pathogenic/Likely pathogenic ★★ same type
- AP4M1 p.Gln183Ter 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-leu393 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown