MATK p.Pro153=
c.459C>T · rs57068027 · VCV747662
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.033%, 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 -8.5 | GERP -3.9 |
| Overall | ||
| CADD | 3.687 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.033%
Middle Eastern · 2/6,060 alleles
Filtering AF
0.00582%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00242%
Overall
0.000682%
11/1,612,676 alleles · ultra-rare
exomes 11/1,460,366 · genomes 0/152,310 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.033% | 3,030 |
| South Asian | 0.0022% | 45,530 |
| Admixed American | 0.00167% | 59,980 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,460 |
| African / African-American | 0.00133% | 75,044 |
| European (non-Finnish) | 0.000339% | 294,951 |
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
- MATK
- Protein
- p.Pro153=
- Coding
- c.459C>T
- MANE Select
- NM_139355
- dbSNP
- rs57068027
- Type
- single nucleotide variant
- Location
- chr19:3783937 (GRCh38)
- Gene constraint
- LOEUF 0.921 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 84.24 · 3 PDB
- Residue 153
- the sh2 domain
Similar variants
- MATK p.Pro153Ala Uncertain significance ★ ⚠ same residue
- MATK p.His34= Likely benign ★★ same type
- MATK p.Pro465= Benign ★★ same type
- MATK p.Ala113Ser Uncertain significance ★ ⚠ same type
- MATK p.Ala132Ser Uncertain significance ★ ⚠ same type
- MATK p.Ala150Thr Uncertain significance ★ ⚠ same type
- MATK p.Ala327Ser Uncertain significance ★ ⚠ same type
- MATK p.Ala466Thr 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/matk-p-pro153 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown