MAP3K7 p.Ser14del
c.21CTC[4] · rs745452796 · VCV2845216
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.221%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.11 | GERP -3.5, phastCons 0.53 |
| Overall | ||
| CADD | 21.0 | PHRED · no single calibrated threshold — expert panels disagree |
| Region caveats | ||
| Repeat context | tandem | GA-rich low complexity · ambiguous alignment · confidence, not pathogenicity |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.221%
Admixed American · 128/57,814 alleles
Filtering AF
0.19%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.178%
Overall
0.0472%
744/1,576,870 alleles · rare
exomes 737/1,424,720 · genomes 7/152,150 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.221% | 452 |
| East Asian | 0.155% | 646 |
| Ashkenazi Jewishnot grpmax-eligible | 0.101% | 987 |
| South Asian | 0.087% | 1,149 |
| Finnishnot grpmax-eligible | 0.0559% | 1,788 |
| African / African-American | 0.0542% | 1,844 |
| Remaining individualsnot grpmax-eligible | 0.0477% | 2,095 |
| Middle Eastern | 0.034% | 2,938 |
| European (non-Finnish) | 0.0292% | 3,420 |
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
- MAP3K7
- Protein
- p.Ser14del
- Coding
- c.21CTC[4]
- MANE Select
- NM_145331
- dbSNP
- rs745452796
- Type
- Microsatellite
- Location
- chr6:90586849 (GRCh38)
- Gene constraint
- LOEUF 0.397 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 70.27 · 25 PDB
- Residue 14
- the 'interaction with mapk8ip1' region
Similar variants
- MAP3K7 p.Ser14_Ala15insSer Uncertain significance ★ same residue
- MAP3K7 p.Ser14_Ala15insSerSer Uncertain significance ★ same residue
- MAP3K7 p.Val50del Pathogenic/Likely pathogenic ★★ same type
- MAP3K7 p.Val42del Likely pathogenic ★ same type
- MAP3K7 p.Cys266del Uncertain significance ★ same type
- MAP3K7 c.121-22_121-12del Likely benign ★ same type
- MAP3K7 c.1211-10_1211-9del Benign ★ same type
- MAP3K7 c.1641-6_1641-3del Likely 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/map3k7-p-ser14del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown