Is SGCD p.Glu170= (c.510G>A) pathogenic?

SGCD p.Glu170= (c.510G>A) is classified Conflicting classifications of pathogenicity in SGCD (ClinVar, Conflicting submitters, 11 submitters; last evaluated 2026-01-28). Rare (popmax 0.133%, mid); Associated with Inborn genetic diseases.

What condition is associated with SGCD p.Glu170= (c.510G>A)?

SGCD p.Glu170= (c.510G>A) is associated with Inborn genetic diseases, cardiomyopathy, autosomal recessive limb-girdle muscular dystrophy type 2F (ClinVar).

How common is SGCD p.Glu170= (c.510G>A) in the general population?

SGCD p.Glu170= (c.510G>A) is rare (popmax 0.133%, mid) (gnomAD).

SGCD p.Glu170=

c.510G>A · rs368838376 · VCV352335

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 11 submitters

gnomAD v4.1

Rare

rare (popmax 0.133%, mid)

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 1.6	GERP -3.4, phastCons 1
Overall
CADD	4.173	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.133% Middle Eastern · 8/6,022 alleles

Filtering AF 0.066% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0482%

Overall 0.0269% 425/1,582,762 alleles · rare exomes 384/1,430,550 · genomes 41/152,212 · joint denominator

Ancestry group	Frequency	1 in
Ashkenazi Jewishnot grpmax-eligible	0.556%	180
Middle Easterngrpmax	0.133%	753
Remaining individualsnot grpmax-eligible	0.0391%	2,557
Admixed American	0.0268%	3,726
European (non-Finnish)	0.0178%	5,615
South Asian	0.0104%	9,639
African / African-American	0.00134%	74,530

Ashkenazi Jewish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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.Glu170=
Coding: c.510G>A
MANE Select: NM_000337
dbSNP: rs368838376
Type: single nucleotide variant
Location: chr5:156647471 (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: cardiomyopathy autosomal recessive limb-girdle muscular dystrophy type 2F qualitative or quantitative defects of delta-sarcoglycan

Similar variants

SGCD p.Glu170Asp 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
SGCD c.4-1G>T 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-glu170 (accessed [today's date]).

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