MAP3K15 p.Arg615=
c.1845A>G · VCV3542816
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0596%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · T>A here scores Δ0.25 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.077 | GERP -4.5, phastCons 0.93 |
| Overall | ||
| CADD | 1.043 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0596%
South Asian · 33/55,393 alleles
Filtering AF
0.0435%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0381%
Overall
0.00287%
34/1,184,006 alleles · ultra-rare
exomes 34/1,070,329 · genomes 0/113,677 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0596% | 1,679 |
| Remaining individualsnot grpmax-eligible | 0.00214% | 46,708 |
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
- MAP3K15
- Protein
- p.Arg615=
- Coding
- c.1845A>G
- MANE Select
- NM_001001671
- Type
- single nucleotide variant
- Location
- chrX:19400663 (GRCh38)
- Structure
- AlphaFold pLDDT 75.41 · 1 PDB
Similar variants
- MAP3K15 p.Ala859Thr Uncertain significance ★★ ⚠ same type
- MAP3K15 p.Ile295Ser Uncertain significance ★★ ⚠ same type
- MAP3K15 p.Leu154Phe Uncertain significance ★★ ⚠ same type
- MAP3K15 p.Thr1229Arg Uncertain significance ★★ ⚠ same type
- MAP3K15 p.Ser199Asn Benign ★★ same type
- MAP3K15 p.Val455Ile Likely benign ★★ same type
- PDHA1 c.*1013C>A Benign ★★ same type
- PDHA1 c.*1059G>A 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/map3k15-p-arg615 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown