Is SGCA p.Val311= (c.933C>T) pathogenic?

SGCA p.Val311= (c.933C>T) is classified Benign in SGCA (ClinVar, Multiple submitters, 14 submitters; last evaluated 2026-02-04). Common (popmax 20.7%, afr) — too common for a highly-penetrant pathogenic allele; Associated with sarcoglycanopathy.

What condition is associated with SGCA p.Val311= (c.933C>T)?

SGCA p.Val311= (c.933C>T) is associated with sarcoglycanopathy, autosomal recessive limb-girdle muscular dystrophy type 2D (ClinVar).

SGCA p.Val311=

Q: How common is SGCA p.Val311= (c.933C>T) in the general population?

SGCA p.Val311= (c.933C>T) is common (popmax 20.7%, afr) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.933C>T · rs1801191 · VCV130294

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 14 submitters

gnomAD v4.1

Common

common (popmax 20.7%, afr) — too common for a highly-penetrant pathogenic allele

Conditions

sarcoglycanopathy

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.284	benign-leaning
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 1.8	GERP 0.82, phastCons 1
Overall
CADD	10.28	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 20.7% African / African-American · 15,507/74,970 alleles

Filtering AF 20.4% ClinGen BA1/BS1 input FAF95, joint · FAF99 20.3%

Overall 4.69% 75,685/1,613,718 alleles · common exomes 62,890/1,461,472 · genomes 12,795/152,246 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	20.7%	5
Remaining individualsnot grpmax-eligible	4.87%	21
Ashkenazi Jewishnot grpmax-eligible	4.63%	22
European (non-Finnish)	4.24%	24
Admixed American	3.46%	29
Finnishnot grpmax-eligible	3.36%	30
Middle Eastern	2.92%	34
Amishnot grpmax-eligible	1.54%	65
South Asian	1.07%	93
East Asian	0.813%	123

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: SGCA
Protein: p.Val311=
Coding: c.933C>T
MANE Select: NM_000023
dbSNP: rs1801191
Type: single nucleotide variant
Location: chr17:50170328 (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

sarcoglycanopathy — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: autosomal recessive limb-girdle muscular dystrophy type 2D

Similar variants

SGCA c.37+6T>C Pathogenic ★★★ same condition
SGCA c.585-1G>A Pathogenic ★★★ same condition
SGCA c.957-11C>G Likely pathogenic ★★★ same condition
SGCA p.Ala107Val Likely pathogenic ★★★ ⚠ same condition
SGCA p.Arg192Ter Pathogenic ★★★ same condition
SGCA p.Arg221Cys Likely pathogenic ★★★ same condition
SGCA p.Arg221Pro Likely pathogenic ★★★ same condition
SGCA p.Arg284Cys 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-val311 (accessed [today's date]).

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