MYRF p.Thr652=
c.1956C>G · VCV4911860
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0165%, mid)
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 -14 | GERP -4.3 |
| Overall | ||
| CADD | 0.062 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0165%
Middle Eastern · 1/6,062 alleles
Filtering AF
0.000247%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000159%
Overall
0.000547%
8/1,461,800 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0165% | 6,062 |
| European (non-Finnish) | 0.000593% | 168,568 |
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.Thr652=
- Coding
- c.1956C>G
- MANE Select
- NM_001127392
- Type
- single nucleotide variant
- Location
- chr11:61778432 (GRCh38)
- Gene constraint
- LOEUF 0.215 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 61.76 · 2 PDB
- Residue 652
- a UniProt-annotated variant site (in cugs; likely pathogenic); the peptidase s74 domain
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-thr652 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown