MAP4 p.Gln1950=
c.5850G>A · rs34711403 · VCV781710
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.19%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.119 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
| Constraint at this position | ||
| Conservation | phyloP -0.12 | GERP -3.8 |
| Overall | ||
| CADD | 0.735 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.19%
Admixed American · 713/60,018 alleles
Filtering AF
1.12%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.09%
Overall
0.91%
14,688/1,614,070 alleles · low-frequency
exomes 13,610/1,461,796 · genomes 1,078/152,274 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 1.19% | 84 |
| European (non-Finnish) | 1.07% | 94 |
| Ashkenazi Jewishnot grpmax-eligible | 1% | 100 |
| Remaining individualsnot grpmax-eligible | 0.896% | 112 |
| Amishnot grpmax-eligible | 0.768% | 130 |
| Middle Eastern | 0.61% | 164 |
| Finnishnot grpmax-eligible | 0.416% | 241 |
| African / African-American | 0.172% | 582 |
| South Asian | 0.0823% | 1,214 |
| East Asian | 0.00446% | 22,438 |
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.Gln1950=
- Coding
- c.5850G>A
- MANE Select
- NM_001385682
- dbSNP
- rs34711403
- Type
- single nucleotide variant
- Location
- chr3:47872008 (GRCh38)
- Gene constraint
- LOEUF 0.512 · pLI 0.14 (gnomAD)
- Structure
- AlphaFold pLDDT 43.03
Similar variants
- MAP4 c.292+9T>G Benign ★★ same type
- MAP4 p.Leu516= Likely benign ★★ same type
- MAP4 p.Val37= Benign ★★ same type
- MAP4 p.Ala150Ser Uncertain significance ★ ⚠ same type
- MAP4 p.Ala1922Val Uncertain significance ★ ⚠ same type
- MAP4 p.Ala1926Pro Uncertain significance ★ ⚠ same type
- MAP4 p.Ala1941Thr Uncertain significance ★ ⚠ same type
- MAP4 p.Ala1959Gly Uncertain significance ★ ⚠ 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/map4-p-gln1950 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown