MRTFA p.Leu897=
c.2691C>T · rs41276311 · VCV773374
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 6 submitters
gnomAD v4.1
Rare
rare (popmax 0.696%, 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 0.26 | GERP -4.5, phastCons 0.92 |
| Overall | ||
| CADD | 0.63 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.696%
European (non-Finnish) · 7,885/1,133,400 alleles
Filtering AF
0.683%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.678%
Overall
0.549%
8,391/1,528,372 alleles · rare
exomes 7,848/1,376,066 · genomes 543/152,306 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.696% | 144 |
| Finnishnot grpmax-eligible | 0.33% | 303 |
| Remaining individualsnot grpmax-eligible | 0.287% | 349 |
| African / African-American | 0.127% | 790 |
| Amishnot grpmax-eligible | 0.11% | 908 |
| Admixed American | 0.0568% | 1,761 |
| South Asian | 0.0177% | 5,640 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00825% | 12,114 |
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.Leu897=
- Coding
- c.2691C>T
- MANE Select
- NM_020831
- dbSNP
- rs41276311
- Type
- single nucleotide variant
- Location
- chr22:40411795 (GRCh38)
- Gene constraint
- LOEUF 0.389 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 56.59 · 2 PDB
- Residue 897
- a UniProt-annotated variant site (in imd66; probable loss-of-function; patient's dendritic cells are morphologically distinct from control dendritic cells and show reduced spreading on fibronectin-coated coverslips, a marked reduction in total f-actin staining and a complete absence of podosomes, a similar phenotype to that of thp1 cells in which mrtfa was silenced)
Similar variants
- MRTFA p.Leu897Phe Uncertain significance ★ ⚠ same residue
- 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
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-leu897 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown