Is FKRP p.Pro90fs (c.267delinsAT) pathogenic?

FKRP p.Pro90fs (c.267delinsAT) is classified Likely pathogenic in FKRP (ClinVar, No assertion criteria, 1 submitter; last evaluated 2017-05-09). No gnomAD frequency available for this variant; Associated with autosomal recessive limb-girdle muscular dystrophy type 2I.

What condition is associated with FKRP p.Pro90fs (c.267delinsAT)?

FKRP p.Pro90fs (c.267delinsAT) is associated with autosomal recessive limb-girdle muscular dystrophy type 2I (ClinVar).

How common is FKRP p.Pro90fs (c.267delinsAT) in the general population?

FKRP p.Pro90fs (c.267delinsAT) is no gnomAD frequency available for this variant (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.

FKRP p.Pro90fs

c.267delinsAT · rs1555738245 · VCV551850

Likely pathogenic No assertion criteria

Classification

Likely pathogenic

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

autosomal recessive limb-girdle muscular dystrophy type 2I

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 -3.1	GERP -2.7

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.Pro90fs
Coding: c.267delinsAT
MANE Select: NM_024301
dbSNP: rs1555738245
Type: Indel
Location: chr19:46755717 (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.Ala336fs Likely pathogenic ★ same condition
FKRP p.Asp74fs Likely pathogenic ★ same condition
FKRP p.Pro186fs Likely pathogenic ★ same condition
FKRP p.Arg167_Cys168delinsSerArg Conflicting classifications of pathogenicity ★ same condition
FKRP p.Pro90Thr Uncertain significance ★ ⚠ same residue
FKRP p.Pro90= Likely benign ★ same residue
FKRP p.Ala397fs Pathogenic ★★ same condition
FKRP p.Ala455Asp 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-pro90fs (accessed [today's date]).

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