MRTFA p.Pro572=
c.1716C>T · rs147775827 · VCV2165327
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0112%, 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 -12 | GERP -4.8 |
| Overall | ||
| CADD | 0.058 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0112%
European (non-Finnish) · 132/1,179,868 alleles
Filtering AF
0.00961%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00904%
Overall
0.00924%
149/1,612,494 alleles · ultra-rare
exomes 141/1,460,354 · genomes 8/152,140 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0112% | 8,938 |
| Remaining individualsnot grpmax-eligible | 0.00961% | 10,407 |
| Admixed American | 0.00834% | 11,996 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,578 |
| Finnishnot grpmax-eligible | 0.00318% | 31,402 |
| African / African-American | 0.00267% | 37,454 |
| East Asian | 0.00223% | 44,866 |
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
- MRTFA
- Protein
- p.Pro572=
- Coding
- c.1716C>T
- MANE Select
- NM_020831
- dbSNP
- rs147775827
- Type
- single nucleotide variant
- Location
- chr22:40419022 (GRCh38)
- Gene constraint
- LOEUF 0.389 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 56.59 · 2 PDB
- Residue 572
- the 'disordered' region
Similar variants
- MRTFA p.Ala352Thr Uncertain significance ★★ ⚠ same type
- MRTFA p.Ala360Thr Uncertain significance ★★ ⚠ same type
- MRTFA p.Ala429Ser Uncertain significance ★★ ⚠ same type
- MRTFA p.Ala479Gly Uncertain significance ★★ ⚠ same type
- MRTFA p.Ala479Val Uncertain significance ★★ ⚠ same type
- MRTFA p.Ala534Thr Uncertain significance ★★ ⚠ same type
- MRTFA p.Ala537Val Uncertain significance ★★ ⚠ same type
- MRTFA p.Ala616Val 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/mrtfa-p-pro572 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown