Is SGCD p.Ala131= (c.393C>T) pathogenic?

SGCD p.Ala131= (c.393C>T) is classified Likely benign in SGCD (ClinVar, Multiple submitters, 7 submitters; last evaluated 2025-12-02). Ultra-rare (popmax 0.0335%, eas); Associated with Inborn genetic diseases.

What condition is associated with SGCD p.Ala131= (c.393C>T)?

SGCD p.Ala131= (c.393C>T) is associated with Inborn genetic diseases, autosomal recessive limb-girdle muscular dystrophy type 2F, dilated cardiomyopathy 1L (ClinVar).

How common is SGCD p.Ala131= (c.393C>T) in the general population?

SGCD p.Ala131= (c.393C>T) is ultra-rare (popmax 0.0335%, eas) (gnomAD).

SGCD p.Ala131=

c.393C>T · rs397517922 · VCV48119

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 7 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0335%, eas)

Conditions

Inborn genetic diseases

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 -3.7	GERP -3.5
Overall
CADD	0.645	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0335% East Asian · 15/44,802 alleles

Filtering AF 0.0206% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0166%

Overall 0.00175% 28/1,603,742 alleles · ultra-rare exomes 23/1,451,786 · genomes 5/151,956 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0335%	2,987
Middle Eastern	0.0165%	6,062
African / African-American	0.00402%	24,889
South Asian	0.00222%	45,011
Remaining individualsnot grpmax-eligible	0.00161%	62,104
European (non-Finnish)	0.000512%	195,455

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: SGCD
Protein: p.Ala131=
Coding: c.393C>T
MANE Select: NM_000337
dbSNP: rs397517922
Type: single nucleotide variant
Location: chr5:156594942 (GRCh38)
Gene constraint: LOEUF 0.88 · pLI 0.05 (gnomAD)
Structure: AlphaFold pLDDT 81.43

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

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: autosomal recessive limb-girdle muscular dystrophy type 2F dilated cardiomyopathy 1L

Similar variants

SGCD p.Ala131Pro Pathogenic same residue
SGCD p.Ala131fs Pathogenic/Likely pathogenic ★★ same residue
SGCD p.Arg165Ter Pathogenic ★★★ same condition
SGCD p.Arg97Ter Pathogenic ★★★ same condition
SGCD p.Arg31Trp Uncertain significance ★★★ ⚠ same condition
SGCD p.Ile64Thr Uncertain significance ★★★ ⚠ same condition
SGCD c.192+1G>A Likely pathogenic ★★ same condition
SGCD c.294+1G>A 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/sgcd-p-ala131 (accessed [today's date]).

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