Is SGCD p.Cys264= (c.792C>T) pathogenic?

SGCD p.Cys264= (c.792C>T) is classified Conflicting classifications of pathogenicity in SGCD (ClinVar, Conflicting submitters, 3 submitters; last evaluated 2025-06-04). Very rare (popmax 0.00933%, afr); Associated with Inborn genetic diseases.

What condition is associated with SGCD p.Cys264= (c.792C>T)?

SGCD p.Cys264= (c.792C>T) is associated with Inborn genetic diseases, autosomal recessive limb-girdle muscular dystrophy type 2F (ClinVar).

How common is SGCD p.Cys264= (c.792C>T) in the general population?

SGCD p.Cys264= (c.792C>T) is very rare (popmax 0.00933%, afr) (gnomAD).

SGCD p.Cys264=

c.792C>T · rs367616773 · VCV597476

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00933%, afr)

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 0.26	GERP -3.1, phastCons 0.98
Overall
CADD	12.04	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00933% African / African-American · 7/75,024 alleles

Filtering AF 0.00437% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0031%

Overall 0.00415% 67/1,613,354 alleles · very rare exomes 58/1,461,074 · genomes 9/152,280 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00933%	10,718
Remaining individualsnot grpmax-eligible	0.0064%	15,614
Admixed American	0.005%	20,000
European (non-Finnish)	0.00441%	22,681
East Asian	0.00223%	44,876

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.Cys264=
Coding: c.792C>T
MANE Select: NM_000337
dbSNP: rs367616773
Type: single nucleotide variant
Location: chr5:156759309 (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

Similar variants

SGCD p.Cys264Arg Uncertain significance ★ ⚠ same residue
SGCD p.Cys264Trp Uncertain significance ★ ⚠ 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-cys264 (accessed [today's date]).

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