Is POMT2 p.Pro79= (c.237G>A) pathogenic?

POMT2 p.Pro79= (c.237G>A) is classified Benign in POMT2 (ClinVar, Single submitter, 1 submitter; last evaluated 2026-01-13). Rare (popmax 0.142%, eas); Associated with muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A2.

What condition is associated with POMT2 p.Pro79= (c.237G>A)?

POMT2 p.Pro79= (c.237G>A) 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.Pro79= (c.237G>A) in the general population?

POMT2 p.Pro79= (c.237G>A) is rare (popmax 0.142%, eas) (gnomAD).

How is Walker-Warburg syndrome inherited?

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

POMT2 p.Pro79=

c.237G>A · rs201322445 · VCV702449

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.142%, eas)

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.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -2.7	GERP -2.8
Overall
CADD	11.54	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.142% East Asian · 58/40,918 alleles

Filtering AF 0.113% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.102%

Overall 0.00414% 64/1,546,458 alleles · rare exomes 50/1,394,154 · genomes 14/152,304 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.142%	705
Remaining individualsnot grpmax-eligible	0.00666%	15,019
Admixed American	0.00196%	51,030
South Asian	0.00119%	84,084

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: POMT2
Protein: p.Pro79=
Coding: c.237G>A
MANE Select: NM_013382
dbSNP: rs201322445
Type: single nucleotide variant
Location: chr14:77320445 (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 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-pro79 (accessed [today's date]).

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