MAP3K19 p.Asn124=
c.372T>C · rs145950712 · VCV2651380
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.676%, mid)
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 0.14 | GERP -1.9 |
| Overall | ||
| CADD | 0.775 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.676%
Middle Eastern · 41/6,062 alleles
Filtering AF
0.512%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.455%
Overall
0.0849%
1,371/1,614,126 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.676% | 148 |
| Admixed American | 0.175% | 572 |
| Remaining individualsnot grpmax-eligible | 0.101% | 992 |
| European (non-Finnish) | 0.0903% | 1,107 |
| South Asian | 0.0626% | 1,598 |
| Finnishnot grpmax-eligible | 0.0297% | 3,369 |
| African / African-American | 0.0253% | 3,949 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,604 |
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
- MAP3K19
- Protein
- p.Asn124=
- Coding
- c.372T>C
- MANE Select
- NM_025052
- dbSNP
- rs145950712
- Type
- single nucleotide variant
- Location
- chr2:134998940 (GRCh38)
- Gene constraint
- LOEUF 0.961 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 44.13
Similar variants
- MAP3K19 p.Gln1309His Uncertain significance ★★ ⚠ same type
- MAP3K19 p.Ala115Val Uncertain significance ★ ⚠ same type
- MAP3K19 p.Ala1214Val Uncertain significance ★ ⚠ same type
- MAP3K19 p.Ala1274Val Uncertain significance ★ ⚠ same type
- MAP3K19 p.Arg1007Thr Uncertain significance ★ ⚠ same type
- MAP3K19 p.Arg1185His Uncertain significance ★ ⚠ same type
- MAP3K19 p.Arg1272Gly Uncertain significance ★ same type
- MAP3K19 p.Arg1283Gln 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/map3k19-p-asn124 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown