MAP4 p.Pro100=
c.300A>G · rs139731146 · VCV3047450
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0334%, afr)
Conditions
1
MAP4-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.024 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.027 | GERP -3.3, phastCons 0.003 |
| Overall | ||
| CADD | 6.611 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0334%
African / African-American · 25/74,940 alleles
Filtering AF
0.0231%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0198%
Overall
0.00161%
26/1,614,002 alleles · ultra-rare
exomes 6/1,461,780 · genomes 20/152,222 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0334% | 2,998 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,480 |
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.Pro100=
- Coding
- c.300A>G
- MANE Select
- NM_001385682
- dbSNP
- rs139731146
- Type
- single nucleotide variant
- Location
- chr3:47928343 (GRCh38)
- Gene constraint
- LOEUF 0.512 · pLI 0.14 (gnomAD)
- Structure
- AlphaFold pLDDT 43.03
- Residue 100
- the 'disordered' region
Disease context
MAP4-related disorder
Similar variants
- 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.Ala2134= Likely benign same condition
- MAP4 p.Ala437= Likely benign same condition
- MAP4 p.Arg23Gln Benign same condition
- MAP4 p.Arg23Trp Likely 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-pro100 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown