Is SGCD p.Tyr28= (c.84T>C) pathogenic?

SGCD p.Tyr28= (c.84T>C) is classified Benign in SGCD (ClinVar, Multiple submitters, 15 submitters; last evaluated 2026-02-04). Common (popmax 79.4%, eas) — too common for a highly-penetrant pathogenic allele; Associated with Inborn genetic diseases.

SGCD p.Tyr28=

Q: What condition is associated with SGCD p.Tyr28= (c.84T>C)?

SGCD p.Tyr28= (c.84T>C) is associated with Inborn genetic diseases, autosomal recessive limb-girdle muscular dystrophy type 2F, qualitative or quantitative defects of delta-sarcoglycan (ClinVar).

Q: How common is SGCD p.Tyr28= (c.84T>C) in the general population?

SGCD p.Tyr28= (c.84T>C) is common (popmax 79.4%, eas) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.84T>C · rs1801193 · VCV48125

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 15 submitters

gnomAD v4.1

Common

common (popmax 79.4%, eas) — too common for a highly-penetrant pathogenic allele

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 -5.4	GERP -3.9
Overall
CADD	1.075	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 79.4% East Asian · 35,524/44,714 alleles

Filtering AF 78.8% ClinGen BA1/BS1 input FAF95, joint · FAF99 78.5%

Overall 44.5% 716,230/1,610,812 alleles · common exomes 654,227/1,458,880 · genomes 62,003/151,932 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	79.4%	1
South Asian	55.7%	2
Middle Eastern	49.6%	2
Ashkenazi Jewishnot grpmax-eligible	48.1%	2
Finnishnot grpmax-eligible	45.7%	2
Remaining individualsnot grpmax-eligible	45.7%	2
Amishnot grpmax-eligible	45.4%	2
Admixed American	44.6%	2
European (non-Finnish)	43.2%	2
African / African-American	26.4%	4

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.Tyr28=
Coding: c.84T>C
MANE Select: NM_000337
dbSNP: rs1801193
Type: single nucleotide variant
Location: chr5:156344569 (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 qualitative or quantitative defects of delta-sarcoglycan

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-tyr28 (accessed [today's date]).

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