MAP3K1 p.Thr1313=
c.3939G>A · rs199940554 · VCV783244
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0175%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -15 | GERP -4.7 |
| Overall | ||
| CADD | 0.137 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0175%
European (non-Finnish) · 207/1,179,826 alleles
Filtering AF
0.0155%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0148%
Overall
0.0146%
235/1,613,810 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0175% | 5,700 |
| South Asian | 0.0121% | 8,279 |
| Remaining individualsnot grpmax-eligible | 0.0112% | 8,927 |
| African / African-American | 0.00933% | 10,719 |
| Admixed American | 0.005% | 20,000 |
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
- MAP3K1
- Protein
- p.Thr1313=
- Coding
- c.3939G>A
- MANE Select
- NM_005921
- dbSNP
- rs199940554
- Type
- single nucleotide variant
- Location
- chr5:56884783 (GRCh38)
- Gene constraint
- LOEUF 0.355 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 59.80 · 1 PDB
- Residue 1313
- the protein kinase domain
Similar variants
- MAP3K1 p.Arg186Gly Pathogenic/Likely pathogenic ★★ ⚠ same type
- MAP3K1 p.Ala594Ser Uncertain significance ★★ ⚠ same type
- MAP3K1 p.Arg204Lys Uncertain significance ★★ ⚠ same type
- MAP3K1 p.Gln548Glu Uncertain significance ★★ ⚠ same type
- MAP3K1 p.Val1346Ile Uncertain significance ★★ ⚠ same type
- MAP3K1 c.1035+12C>T Likely benign ★★ same type
- MAP3K1 c.1687-46C>G Benign ★★ same type
- MAP3K1 c.2088-92C>T 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/map3k1-p-thr1313 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown