MYRF p.Ser388=
c.1164G>A · VCV3298163
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00223%, eas)
Conditions
1
Inborn genetic diseases
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.54 | acceptor gain · deltas |
|---|---|---|
| Pangolin | Δ0.29 | gain · loss 0.03 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP -3.9 | GERP -4.6 |
| Overall | ||
| CADD | 17.36 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00223%
East Asian · 1/44,864 alleles
Overall
0.000124%
2/1,613,434 alleles · very rare
exomes 2/1,461,170 · genomes 0/152,264 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00223% | 44,864 |
| European (non-Finnish) | 8.47e-05% | 1,179,970 |
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.Ser388=
- Coding
- c.1164G>A
- MANE Select
- NM_001127392
- Type
- single nucleotide variant
- Location
- chr11:61774015 (GRCh38)
- Gene constraint
- LOEUF 0.215 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 61.76 · 2 PDB
- Residue 388
- a β-strand; a DNA-binding region
Similar variants
- MYRF p.Ala1001Ser Uncertain significance ★★ ⚠ same condition
- MYRF p.Arg174Cys Uncertain significance ★★ ⚠ same condition
- MYRF p.Arg733Gln Uncertain significance ★★ ⚠ same condition
- MYRF p.Asn267Ser Uncertain significance ★★ ⚠ same condition
- MYRF p.Pro743Ser Uncertain significance ★★ ⚠ same condition
- MYRF p.Thr1102Ile Uncertain significance ★★ ⚠ same condition
- MYRF p.Gly96Ser Likely benign ★★ same condition
- MYRF p.Gln403Ter Pathogenic ★ same condition
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-ser388 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown