Is SGCD p.Val48= (c.144G>C) pathogenic?

SGCD p.Val48= (c.144G>C) is classified Benign/Likely benign in SGCD (ClinVar, Multiple submitters, 11 submitters; last evaluated 2026-01-27). Rare (popmax 0.346%, afr); Associated with cardiomyopathy.

What condition is associated with SGCD p.Val48= (c.144G>C)?

SGCD p.Val48= (c.144G>C) is associated with cardiomyopathy, autosomal recessive limb-girdle muscular dystrophy type 2F, dilated cardiomyopathy 1L (ClinVar).

How common is SGCD p.Val48= (c.144G>C) in the general population?

SGCD p.Val48= (c.144G>C) is rare (popmax 0.346%, afr) (gnomAD).

SGCD p.Val48=

c.144G>C · rs372152495 · VCV139099

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 11 submitters

gnomAD v4.1

Rare

rare (popmax 0.346%, afr)

Conditions

cardiomyopathy

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 8.5	GERP 1, phastCons 1
Overall
CADD	8.45	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.346% African / African-American · 259/74,860 alleles

Filtering AF 0.311% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.298%

Overall 0.0172% 278/1,611,860 alleles · rare exomes 136/1,459,650 · genomes 142/152,210 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.346%	289
Remaining individualsnot grpmax-eligible	0.0128%	7,803
Admixed American	0.00836%	11,955
South Asian	0.00221%	45,272
European (non-Finnish)	0.000339%	294,746

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.Val48=
Coding: c.144G>C
MANE Select: NM_000337
dbSNP: rs372152495
Type: single nucleotide variant
Location: chr5:156344629 (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

cardiomyopathy — 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.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
SGCD c.4-1G>T Likely pathogenic ★★ same condition
SGCD p.Arg33Ter 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/sgcd-p-val48 (accessed [today's date]).

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