Is POMT2 p.Pro696= (c.2088C>T) pathogenic?

POMT2 p.Pro696= (c.2088C>T) is classified Likely benign in POMT2 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-12-05). No allele count reported in gnomAD v4.1 (AN 1,506,720); Associated with muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A2.

What condition is associated with POMT2 p.Pro696= (c.2088C>T)?

POMT2 p.Pro696= (c.2088C>T) is associated with muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A2, muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B2, autosomal recessive limb-girdle muscular dystrophy type 2N (ClinVar).

How common is POMT2 p.Pro696= (c.2088C>T) in the general population?

POMT2 p.Pro696= (c.2088C>T) is no allele count reported in gnomAD v4.1 (AN 1,506,720) (gnomAD).

How is Walker-Warburg syndrome inherited?

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

POMT2 p.Pro696=

c.2088C>T · rs1389415600 · VCV2930830

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,506,720)

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.
REVEL	0.198	benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.48	GERP -2.9
Overall
CADD	0.921	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,506,720). 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.Pro696=
Coding: c.2088C>T
MANE Select: NM_013382
dbSNP: rs1389415600
Type: single nucleotide variant
Location: chr14:77278453 (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

Also linked: muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B2 autosomal recessive limb-girdle muscular dystrophy type 2N

For Walker-Warburg syndrome (Orphanet):

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

Similar variants

POMT2 p.Pro696Thr Uncertain significance ★★ ⚠ same residue
POMT2 p.Pro696Leu Uncertain significance ★ ⚠ same residue
POMT2 p.Pro696Ser Uncertain significance ★ ⚠ same residue
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

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-pro696 (accessed [today's date]).

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