MAP3K5 p.Cys1005=
c.3015C>T · rs150394997 · VCV734375
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.86%, sas)
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 -6 | GERP -3.8 |
| Overall | ||
| CADD | 0.322 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.86%
South Asian · 783/91,066 alleles
Filtering AF
0.81%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.79%
Overall
0.131%
2,113/1,613,878 alleles · rare
exomes 1,985/1,461,868 · genomes 128/152,010 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.86% | 116 |
| Middle Eastern | 0.182% | 551 |
| Remaining individualsnot grpmax-eligible | 0.155% | 644 |
| European (non-Finnish) | 0.0975% | 1,026 |
| Admixed American | 0.05% | 2,000 |
| African / African-American | 0.0347% | 2,882 |
| East Asian | 0.0268% | 3,737 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00676% | 14,801 |
| Finnishnot grpmax-eligible | 0.00313% | 31,984 |
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
- MAP3K5
- Protein
- p.Cys1005=
- Coding
- c.3015C>T
- MANE Select
- NM_005923
- dbSNP
- rs150394997
- Type
- single nucleotide variant
- Location
- chr6:136592478 (GRCh38)
- Gene constraint
- LOEUF 0.433 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 73.87 · 27 PDB
- Residue 1005
- the 'interaction with ppia/cypa' region
Similar variants
- MAP3K5 p.Ala1162Val Uncertain significance ★ ⚠ same type
- MAP3K5 p.Ala1166Val Uncertain significance ★ ⚠ same type
- MAP3K5 p.Ala1322Val Uncertain significance ★ ⚠ same type
- MAP3K5 p.Ala283Val Uncertain significance ★ ⚠ same type
- MAP3K5 p.Ala422Pro Uncertain significance ★ ⚠ same type
- MAP3K5 p.Ala909Thr Uncertain significance ★ ⚠ same type
- MAP3K5 p.Arg1014Gln Uncertain significance ★ ⚠ same type
- MAP3K5 p.Arg1239Trp 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/map3k5-p-cys1005 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown