Is FKRP p.Pro89Arg (c.266C>G) pathogenic?

FKRP p.Pro89Arg (c.266C>G) is classified Likely pathogenic in FKRP (ClinVar, Single submitter, 1 submitter; last evaluated 2024-09-09). AlphaMissense: likely pathogenic (0.9192); Absent from gnomAD v4.1; Associated with autosomal recessive limb-girdle muscular dystrophy type 2I.

What condition is associated with FKRP p.Pro89Arg (c.266C>G)?

FKRP p.Pro89Arg (c.266C>G) is associated with autosomal recessive limb-girdle muscular dystrophy type 2I (ClinVar).

How common is FKRP p.Pro89Arg (c.266C>G) in the general population?

FKRP p.Pro89Arg (c.266C>G) is absent from gnomAD v4.1 (gnomAD).

How is FKRP-related limb-girdle muscular dystrophy R9 inherited?

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

What do computational predictors say about FKRP p.Pro89Arg (c.266C>G)?

AlphaMissense predicts likely pathogenic (score 0.9192) — an in-silico prediction, not a clinical call.

FKRP p.Pro89Arg

c.266C>G · VCV4816131

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9192 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,576,736)

Missense predictors

2/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

autosomal recessive limb-girdle muscular dystrophy type 2I

Computational evidence

Protein change
AlphaMissense	0.9192	likely pathogenic ✓ concordant with ClinVar
REVEL	0.935	strongly pathogenic-leaning
SaProt	LLR -9.19	tolerated
⇒ AlphaMissense and REVEL call this damaging; SaProt does not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.4	GERP 1.4, phastCons 1
Regional constraint	o/e 1.06	unconstrained · MANE · 1,484 bp · p 0.11 · regional, not allelic
Overall
CADD	25.1	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,576,736). 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.Pro89Arg
Coding: c.266C>G
MANE Select: NM_024301
Type: single nucleotide variant
Location: chr19:46755716 (GRCh38)
Gene constraint: LOEUF 1.543 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 94.08 · 8 PDB

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

Disease context

autosomal recessive limb-girdle muscular dystrophy type 2I — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For FKRP-related limb-girdle muscular dystrophy R9 (Orphanet):

Inheritance: Autosomal recessive
Onset: Adolescent, Adult, Childhood
Prevalence: 1-9 / 100 000 (Europe)

Similar variants

FKRP p.Pro89Ala Pathogenic/Likely pathogenic ★★ ⚠ same residue
FKRP p.Pro89Leu Pathogenic/Likely pathogenic ★★ ⚠ same residue
FKRP p.Pro89Ser Likely pathogenic ★★ same residue
FKRP p.Pro89= Likely benign ★★ same residue
FKRP p.Ala455Asp Pathogenic ★★ same condition
FKRP p.Arg176Ter Pathogenic/Likely pathogenic ★★ same condition
FKRP p.Arg275Cys Pathogenic/Likely pathogenic ★★ same condition
FKRP p.Asn463Asp 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-pro89arg (accessed [today's date]).

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