Is FKRP p.Phe223fs (c.668_669del) pathogenic?

FKRP p.Phe223fs (c.668669del) is classified Likely pathogenic in FKRP (ClinVar, Single submitter, 1 submitter; last evaluated 2023-11-26). No gnomAD frequency available for this variant; Associated with muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A5.

How common is FKRP p.Phe223fs (c.668_669del) in the general population?

FKRP p.Phe223fs (c.668_669del) is no gnomAD frequency available for this variant (gnomAD).

How is Walker-Warburg syndrome inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

FKRP p.Phe223fs

Q: What condition is associated with FKRP p.Phe223fs (c.668_669del)?

FKRP p.Phe223fs (c.668_669del) is associated with muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A5 (ClinVar).

c.668_669del · rs2513990753 · VCV3241631

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A5

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	escapes	premature termination codon in the last exon (4 of 4) — the truncated protein is likely expressed. PVS1 input, not an applied code
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 0.49	GERP -1.6, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: FKRP
Protein: p.Phe223fs
Coding: c.668_669del
MANE Select: NM_024301
dbSNP: rs2513990753
Type: Deletion
Location: chr19:46756117 (GRCh38)
Gene constraint: LOEUF 1.543 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 94.08 · 8 PDB
Residue 223: an α-helix

Full FKRP gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A5 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Walker-Warburg syndrome (Orphanet):

Inheritance: Autosomal recessive
Onset: Antenatal, Infancy, Neonatal
Prevalence: <1 / 1 000 000 (United Kingdom)

Similar variants

FKRP p.Ala150fs Pathogenic ★★ same condition
FKRP p.Arg423fs Pathogenic/Likely pathogenic ★★ same condition
FKRP p.Leu171fs Pathogenic/Likely pathogenic ★★ same condition
FKRP p.Leu238fs Pathogenic/Likely pathogenic ★★ same condition
FKRP p.Leu446fs Pathogenic/Likely pathogenic ★★ same condition
FKRP p.Lys472fs Pathogenic/Likely pathogenic ★★ same condition
FKRP p.Ser211fs Likely pathogenic ★★ same condition
FKRP p.Ser69del 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-phe223fs (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown