Is POMT2 p.Phe563= (c.1689C>T) pathogenic?

POMT2 p.Phe563= (c.1689C>T) is classified Likely benign in POMT2 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-12-31). Absent from gnomAD v4.1; Associated with autosomal recessive limb-girdle muscular dystrophy type 2N.

How common is POMT2 p.Phe563= (c.1689C>T) in the general population?

POMT2 p.Phe563= (c.1689C>T) is absent from gnomAD v4.1 (gnomAD).

How is POMT2-related limb-girdle muscular dystrophy R14 inherited?

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

POMT2 p.Phe563=

Q: What condition is associated with POMT2 p.Phe563= (c.1689C>T)?

POMT2 p.Phe563= (c.1689C>T) is associated with autosomal recessive limb-girdle muscular dystrophy type 2N, muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A2, muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B2 (ClinVar).

c.1689C>T · VCV3760155

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

autosomal recessive limb-girdle muscular dystrophy type 2N

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.3	indeterminate
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 4.5	GERP 0.66, phastCons 1
Overall
CADD	10.35	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: POMT2
Protein: p.Phe563=
Coding: c.1689C>T
MANE Select: NM_013382
Type: single nucleotide variant
Location: chr14:77280428 (GRCh38)
Gene constraint: LOEUF 0.944 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 87.96

Full POMT2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

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

Also linked: muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A2 muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B2

For POMT2-related limb-girdle muscular dystrophy R14 (Orphanet):

Inheritance: Autosomal recessive
Onset: Infancy
Prevalence: <1 / 1 000 000 (Worldwide)

Similar variants

POMT2 c.1006+1G>A Pathogenic ★★ same condition
POMT2 c.1184-1G>C Likely pathogenic ★★ same condition
POMT2 c.1254-2A>G Likely pathogenic ★★ same condition
POMT2 c.1333-14G>A Pathogenic/Likely pathogenic ★★ same condition
POMT2 c.1786-2A>T Pathogenic/Likely pathogenic ★★ same condition
POMT2 c.248+1G>A Likely pathogenic ★★ same condition
POMT2 c.248+1G>C Pathogenic/Likely pathogenic ★★ same condition
POMT2 c.248+1G>T 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/pomt2-p-phe563 (accessed [today's date]).

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