Is SGCA p.Pro257fs (c.770del) pathogenic?

SGCA p.Pro257fs (c.770del) is classified Pathogenic in SGCA (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-03-13). No gnomAD frequency available for this variant; Associated with autosomal recessive limb-girdle muscular dystrophy type 2D.

What condition is associated with SGCA p.Pro257fs (c.770del)?

SGCA p.Pro257fs (c.770del) is associated with autosomal recessive limb-girdle muscular dystrophy type 2D (ClinVar).

How common is SGCA p.Pro257fs (c.770del) in the general population?

SGCA p.Pro257fs (c.770del) is no gnomAD frequency available for this variant (gnomAD).

SGCA p.Pro257fs

Q: How is Alpha-sarcoglycan-related limb-girdle muscular dystrophy R3 inherited?

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

c.770del · rs886043962 · VCV288637

Pathogenic Multiple submitters

Classification

Pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

autosomal recessive limb-girdle muscular dystrophy type 2D

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 7 of 10
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 1.7	GERP 0.8, phastCons 1

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: SGCA
Protein: p.Pro257fs
Coding: c.770del
MANE Select: NM_000023
dbSNP: rs886043962
Type: Deletion
Location: chr17:50170164 (GRCh38)
Gene constraint: LOEUF 1.273 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 80.15

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

Disease context

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

For Alpha-sarcoglycan-related limb-girdle muscular dystrophy R3 (Orphanet):

Inheritance: Autosomal recessive
Onset: Adolescent, Childhood
Prevalence: <1 / 1 000 000 (United Kingdom)

Similar variants

SGCA p.Pro257= Likely benign ★ same residue
SGCA p.Asp385fs Uncertain significance ★★★ same condition
SGCA c.586delG Pathogenic/Likely pathogenic ★★ same condition
SGCA c.956+2_956+19del Likely pathogenic ★★ same condition
SGCA p.Ala57fs Pathogenic ★★ same condition
SGCA p.Asp266fs Pathogenic/Likely pathogenic ★★ same condition
SGCA p.Gly68fs Pathogenic/Likely pathogenic ★★ same condition
SGCA p.Leu131fs 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/sgca-p-pro257fs (accessed [today's date]).

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