Is SGCD p.Glu190Ter (c.568G>T) pathogenic?

SGCD p.Glu190Ter (c.568G>T) is classified Pathogenic in SGCD (ClinVar, Single submitter, 1 submitter; last evaluated 2021-07-10). No allele count reported in gnomAD v4.1 (AN 1,574,326); Associated with Abnormality of the musculature.

What condition is associated with SGCD p.Glu190Ter (c.568G>T)?

SGCD p.Glu190Ter (c.568G>T) is associated with Abnormality of the musculature (ClinVar).

How common is SGCD p.Glu190Ter (c.568G>T) in the general population?

SGCD p.Glu190Ter (c.568G>T) is no allele count reported in gnomAD v4.1 (AN 1,574,326) (gnomAD).

SGCD p.Glu190Ter

c.568G>T · rs1412814368 · VCV1180701

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

nonsense (stop-gain)

predicted LoF

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,574,326)

Conditions

Abnormality of the musculature

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	nonsense (stop-gain)	predicted loss-of-function
NMD	predicted	premature termination codon in exon 7 of 9
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Pangolin	Δ0.20	loss · gain 0.00 · not in the SpliceAI release · independent
Constraint at this position
Conservation	phyloP 9.8	GERP 2.7, phastCons 1
Overall
CADD	46.0	PHRED · no single calibrated threshold — expert panels disagree

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,574,326). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: SGCD
Protein: p.Glu190Ter
Coding: c.568G>T
MANE Select: NM_000337
dbSNP: rs1412814368
Type: single nucleotide variant
Location: chr5:156647529 (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

Abnormality of the musculature — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

SGCD p.Thr143fs Likely pathogenic ★ same condition
SGCD p.Arg165Ter Pathogenic ★★★ same type
SGCD p.Arg97Ter Pathogenic ★★★ same type
SGCD p.Arg31Gly Uncertain significance ★★★ ⚠ same type
SGCD p.Arg31Trp Uncertain significance ★★★ ⚠ same type
SGCD p.Ile64Thr Uncertain significance ★★★ ⚠ same type
SGCD c.192+1G>A Likely pathogenic ★★ same type
SGCD c.294+1G>A Likely pathogenic ★★ same type

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-glu190ter (accessed [today's date]).

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