MAP4 p.Ala2134=
c.6402G>A · rs200032630 · VCV3032804
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.16%, eas)
Conditions
1
MAP4-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.17 | GERP -4.5, phastCons 0.28 |
| Overall | ||
| CADD | 9.598 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.16%
East Asian · 72/44,864 alleles
Filtering AF
0.131%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.12%
Overall
0.00683%
110/1,610,408 alleles · rare
exomes 88/1,458,128 · genomes 22/152,280 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.16% | 623 |
| Middle Eastern | 0.0165% | 6,050 |
| South Asian | 0.0132% | 7,583 |
| Remaining individualsnot grpmax-eligible | 0.00802% | 12,476 |
| Admixed American | 0.005% | 20,003 |
| European (non-Finnish) | 0.00144% | 69,213 |
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
- MAP4
- Protein
- p.Ala2134=
- Coding
- c.6402G>A
- MANE Select
- NM_001385682
- dbSNP
- rs200032630
- Type
- single nucleotide variant
- Location
- chr3:47869220 (GRCh38)
- Gene constraint
- LOEUF 0.512 · pLI 0.14 (gnomAD)
- Structure
- AlphaFold pLDDT 43.03
Disease context
MAP4-related disorder
Similar variants
- MAP4 p.Ala2134Glu Uncertain significance ★ ⚠ same residue
- MAP4 p.Ala2134Val Uncertain significance ★ ⚠ same residue
- MAP4 c.292+2409G>A Likely benign same condition
- MAP4 c.*100G>A Likely benign same condition
- MAP4 c.*44G>A Likely benign same condition
- MAP4 p.Ala2123= Likely benign same condition
- MAP4 p.Ala437= Likely benign same condition
- MAP4 p.Arg23Gln Benign 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/map4-p-ala2134 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown