MRTFB p.Ser439=
c.1317C>T · rs150298259 · VCV710612
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0333%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -5.5 | GERP -4.6 |
| Overall | ||
| CADD | 3.563 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0333%
Admixed American · 20/60,024 alleles
Filtering AF
0.0221%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0184%
Overall
0.0103%
167/1,614,140 alleles · ultra-rare
exomes 149/1,461,884 · genomes 18/152,256 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0333% | 3,001 |
| South Asian | 0.0165% | 6,072 |
| Remaining individualsnot grpmax-eligible | 0.0112% | 8,929 |
| European (non-Finnish) | 0.0102% | 9,833 |
| African / African-American | 0.004% | 25,007 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,602 |
| East Asian | 0.00223% | 44,888 |
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
- MRTFB
- Protein
- p.Ser439=
- Coding
- c.1317C>T
- MANE Select
- NM_001308142
- dbSNP
- rs150298259
- Type
- single nucleotide variant
- Location
- chr16:14246577 (GRCh38)
- Gene constraint
- LOEUF 0.351 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 53.38
Similar variants
- MRTFB p.Asn47= Benign/Likely benign ★★ same type
- MRTFB p.Ser643= Benign ★★ same type
- MRTFB p.Thr9= Benign ★★ same type
- MRTFB p.Ala91Pro Pathogenic ★ same type
- MRTFB p.Leu160Pro Likely pathogenic ★ same type
- MRTFB c.693+1G>T Uncertain significance ★ same type
- MRTFB p.Ala1080Val Uncertain significance ★ same type
- MRTFB p.Ala138Glu 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/mrtfb-p-ser439 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown