MRTFA p.Leu1018=
c.3054C>T · rs148865274 · VCV720853
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 5 submitters
gnomAD v4.1
Rare
rare (popmax 0.449%, eas)
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 -5.6 | GERP -5.1 |
| Overall | ||
| CADD | 0.707 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.449%
East Asian · 198/44,114 alleles
Filtering AF
0.398%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.378%
Overall
0.125%
1,978/1,582,260 alleles · rare
exomes 1,768/1,429,972 · genomes 210/152,288 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.449% | 223 |
| Finnishnot grpmax-eligible | 0.155% | 647 |
| Remaining individualsnot grpmax-eligible | 0.13% | 771 |
| European (non-Finnish) | 0.128% | 780 |
| South Asian | 0.101% | 987 |
| Ashkenazi Jewishnot grpmax-eligible | 0.053% | 1,887 |
| Middle Eastern | 0.0168% | 5,942 |
| Admixed American | 0.012% | 8,327 |
| African / African-American | 0.0094% | 10,635 |
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.Leu1018=
- Coding
- c.3054C>T
- MANE Select
- NM_020831
- dbSNP
- rs148865274
- Type
- single nucleotide variant
- Location
- chr22:40411432 (GRCh38)
- Gene constraint
- LOEUF 0.389 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 56.59 · 2 PDB
Similar variants
- MRTFA p.Leu1018Pro 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-leu1018 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown