Is POMT2 p.Val55fs (c.163dup) pathogenic?

POMT2 p.Val55fs (c.163dup) is classified Likely pathogenic in POMT2 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-05-26). No gnomAD frequency available for this variant; Associated with muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A2.

How common is POMT2 p.Val55fs (c.163dup) in the general population?

POMT2 p.Val55fs (c.163dup) 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.

POMT2 p.Val55fs

Q: What condition is associated with POMT2 p.Val55fs (c.163dup)?

POMT2 p.Val55fs (c.163dup) is associated with muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A2 (ClinVar).

c.163dup · rs2503370602 · VCV2678030

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 A2

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 1 of 21
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 1.6	GERP -1.6, phastCons 0.54

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: POMT2
Protein: p.Val55fs
Coding: c.163dup
MANE Select: NM_013382
dbSNP: rs2503370602
Type: Duplication
Location: chr14:77320518 (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

muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A2 — 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

POMT2 c.1726-1dup Pathogenic/Likely pathogenic ★★ same condition
POMT2 p.Asn553fs Pathogenic/Likely pathogenic ★★ same condition
POMT2 p.Ile572fs Pathogenic/Likely pathogenic ★★ same condition
POMT2 p.Met432fs Pathogenic/Likely pathogenic ★★ same condition
POMT2 p.Phe147fs Pathogenic/Likely pathogenic ★★ same condition
POMT2 p.Tyr376fs Pathogenic ★★ same condition
POMT2 p.Arg27fs Likely pathogenic ★ same condition
POMT2 p.Gln24fs 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-val55fs (accessed [today's date]).

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