FKRP p.Val79=
c.237G>A · rs2513986498 · VCV2034621
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
muscular dystrophy-dystroglycanopathy, type A
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 1.2 | GERP -0.86, phastCons 1 |
| Overall | ||
| CADD | 5.492 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- FKRP
- Protein
- p.Val79=
- Coding
- c.237G>A
- MANE Select
- NM_024301
- dbSNP
- rs2513986498
- Type
- single nucleotide variant
- Location
- chr19:46755687 (GRCh38)
- Gene constraint
- LOEUF 1.543 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 94.08 · 8 PDB
- Residue 79
- a UniProt-annotated variant site (in mddgc5); a β-strand
Disease context
muscular dystrophy-dystroglycanopathy, type A — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Walker-Warburg syndrome (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Antenatal, Infancy, Neonatal
- Prevalence
- <1 / 1 000 000 (United Kingdom)
Similar variants
- FKRP p.Val79Ala Uncertain significance ★★ ⚠ same residue
- FKRP p.Val79Leu Uncertain significance ★ ⚠ same residue
- FKRP p.Val79Met Conflicting classifications of pathogenicity ★ same residue
- FKRP p.Val79fs Pathogenic ★ same residue
- FKRP p.Ala157Pro Pathogenic/Likely pathogenic ★★ same condition
- FKRP p.Ala321Glu Pathogenic/Likely pathogenic ★★ ⚠ same condition
- FKRP p.Ala455Asp Pathogenic ★★ same condition
- FKRP p.Arg176Ter Pathogenic/Likely 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/fkrp-p-val79 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown