MYRF p.Pro1069=
c.3207C>T · rs370887875 · VCV722194
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.5%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.20 | acceptor gain · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -8 | GERP -3.8 |
| Overall | ||
| CADD | 8.004 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.5%
South Asian · 3,189/91,040 alleles
Filtering AF
3.4%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.36%
Overall
0.213%
3,443/1,613,882 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 3.5% | 29 |
| Remaining individualsnot grpmax-eligible | 0.238% | 419 |
| Middle Eastern | 0.148% | 674 |
| Admixed American | 0.00833% | 12,002 |
| European (non-Finnish) | 0.00729% | 13,721 |
| African / African-American | 0.00667% | 14,999 |
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
- MYRF
- Protein
- p.Pro1069=
- Coding
- c.3207C>T
- MANE Select
- NM_001127392
- dbSNP
- rs370887875
- Type
- single nucleotide variant
- Location
- chr11:61784292 (GRCh38)
- Gene constraint
- LOEUF 0.215 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 61.76 · 2 PDB
- Residue 1069
- a UniProt-annotated variant site (in cugs; likely pathogenic); a UniProt-annotated variant site (in nno1; likely pathogenic)
Similar variants
- MYRF p.Gln150Ter Pathogenic/Likely pathogenic ★★ same type
- MYRF p.Trp939Ter Pathogenic ★★ same type
- MYRF p.Ala1001Ser Uncertain significance ★★ ⚠ same type
- MYRF p.Arg174Cys Uncertain significance ★★ ⚠ same type
- MYRF p.Arg733Gln Uncertain significance ★★ ⚠ same type
- MYRF p.Asn267Ser Uncertain significance ★★ ⚠ same type
- MYRF p.Glu421Lys Uncertain significance ★★ ⚠ same type
- MYRF p.Pro743Ser 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/myrf-p-pro1069 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown