MAP4 p.Val1822=
c.5466G>C · rs35521469 · VCV3039645
Benign
No assertion criteria
Classification
Benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.68%, sas)
Conditions
1
MAP4-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.013 | strongly benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
| Constraint at this position | ||
| Conservation | phyloP -0.43 | GERP -3.8 |
| Overall | ||
| CADD | 0.766 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.68%
South Asian · 1,527/91,048 alleles
Filtering AF
1.61%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.58%
Overall
0.212%
3,422/1,613,974 alleles · low-frequency
exomes 3,185/1,461,738 · genomes 237/152,236 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 1.68% | 60 |
| Ashkenazi Jewishnot grpmax-eligible | 1.63% | 62 |
| Middle Eastern | 0.876% | 114 |
| Remaining individualsnot grpmax-eligible | 0.315% | 317 |
| European (non-Finnish) | 0.0954% | 1,048 |
| Admixed American | 0.045% | 2,223 |
| African / African-American | 0.012% | 8,334 |
| East Asian | 0.00223% | 44,866 |
| Finnishnot grpmax-eligible | 0.00156% | 64,012 |
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.Val1822=
- Coding
- c.5466G>C
- MANE Select
- NM_001385682
- dbSNP
- rs35521469
- Type
- single nucleotide variant
- Location
- chr3:47877492 (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-val1822 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown