MAP4K4 p.Tyr85=
c.255T>C · rs55856263 · VCV711192
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.117%, amr)
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 -0.8 | GERP -4.6, phastCons 0.011 |
| Overall | ||
| CADD | 4.299 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.117%
Admixed American · 70/59,612 alleles
Filtering AF
0.0953%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0872%
Overall
0.0233%
375/1,606,198 alleles · rare
exomes 343/1,454,204 · genomes 32/151,994 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.117% | 852 |
| Middle Eastern | 0.0663% | 1,508 |
| Remaining individualsnot grpmax-eligible | 0.0386% | 2,593 |
| European (non-Finnish) | 0.0233% | 4,286 |
| African / African-American | 0.00402% | 24,892 |
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
- MAP4K4
- Protein
- p.Tyr85=
- Coding
- c.255T>C
- MANE Select
- NM_001395002
- dbSNP
- rs55856263
- Type
- single nucleotide variant
- Location
- chr2:101824002 (GRCh38)
- Gene constraint
- LOEUF 0.308 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 66.47 · 19 PDB
- Residue 85
- the protein kinase domain; a β-strand
Similar variants
- MAP4K4 p.Arg1329Ter Pathogenic/Likely pathogenic ★★ same type
- MAP4K4 p.Ala491Pro Uncertain significance ★★ ⚠ same type
- MAP4K4 p.Arg1135Cys Uncertain significance ★★ ⚠ same type
- MAP4K4 p.Leu742Pro Uncertain significance ★★ ⚠ same type
- MAP4K4 p.Ser758Phe Uncertain significance ★★ ⚠ same type
- MAP4K4 c.1022+125A>G Benign ★★ same type
- MAP4K4 c.123+57A>G Benign ★★ same type
- MAP4K4 c.1234-81C>G Benign ★★ 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/map4k4-p-tyr85 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown