MAP4 p.Glu20=
c.60G>A · rs201700598 · VCV3035813
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.231%, mid)
Conditions
1
MAP4-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.116 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
| Constraint at this position | ||
| Conservation | phyloP 0.81 | GERP -0.24, phastCons 1 |
| Overall | ||
| CADD | 8.159 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.231%
Middle Eastern · 14/6,062 alleles
Filtering AF
0.14%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.112%
Overall
0.00372%
60/1,614,188 alleles · rare
exomes 53/1,461,876 · genomes 7/152,312 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.231% | 433 |
| Remaining individualsnot grpmax-eligible | 0.0144% | 6,946 |
| South Asian | 0.00769% | 13,011 |
| Admixed American | 0.005% | 20,005 |
| African / African-American | 0.00267% | 37,523 |
| European (non-Finnish) | 0.00212% | 47,202 |
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.Glu20=
- Coding
- c.60G>A
- MANE Select
- NM_001385682
- dbSNP
- rs201700598
- Type
- single nucleotide variant
- Location
- chr3:47998801 (GRCh38)
- Gene constraint
- LOEUF 0.512 · pLI 0.14 (gnomAD)
- Structure
- AlphaFold pLDDT 43.03
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-glu20 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown