Is SGCD p.Thr281= (c.843T>C) pathogenic?

SGCD p.Thr281= (c.843T>C) is classified Likely benign in SGCD (ClinVar, No assertion criteria, 1 submitter; last evaluated 2024-04-09). Absent from gnomAD v4.1; Associated with SGCD-related disorder.

What condition is associated with SGCD p.Thr281= (c.843T>C)?

SGCD p.Thr281= (c.843T>C) is associated with SGCD-related disorder (ClinVar).

How common is SGCD p.Thr281= (c.843T>C) in the general population?

SGCD p.Thr281= (c.843T>C) is absent from gnomAD v4.1 (gnomAD).

SGCD p.Thr281=

c.843T>C · VCV3347343

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

SGCD-related disorder

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 -0.79	GERP -5.4, phastCons 0.015
Overall
CADD	4.944	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: SGCD
Protein: p.Thr281=
Coding: c.843T>C
MANE Select: NM_000337
Type: single nucleotide variant
Location: chr5:156759360 (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

SGCD-related disorder

Similar variants

SGCD p.Thr281Ala Uncertain significance ★ ⚠ same residue
SGCD p.Arg33Ter Pathogenic/Likely pathogenic ★★ same condition
SGCD c.4-1G>A Conflicting classifications of pathogenicity ★ same condition
SGCD p.Tyr23His Uncertain significance ★ ⚠ same condition
SGCD c.383-40C>T Likely benign same condition
SGCD c.383-34_383-28del Likely benign same condition
SGCD c.383-56TC[7] Likely benign same condition
SGCD c.383-56TC[9] Likely benign 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-thr281 (accessed [today's date]).

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