Is SGCD p.Tyr90= (c.270C>T) pathogenic?

SGCD p.Tyr90= (c.270C>T) is classified Conflicting classifications of pathogenicity in SGCD (ClinVar, Conflicting submitters, 5 submitters; last evaluated 2026-04-02). Very rare (popmax 0.00667%, sas); Associated with Inborn genetic diseases.

What condition is associated with SGCD p.Tyr90= (c.270C>T)?

SGCD p.Tyr90= (c.270C>T) is associated with Inborn genetic diseases, autosomal recessive limb-girdle muscular dystrophy type 2F (ClinVar).

How common is SGCD p.Tyr90= (c.270C>T) in the general population?

SGCD p.Tyr90= (c.270C>T) is very rare (popmax 0.00667%, sas) (gnomAD).

SGCD p.Tyr90=

c.270C>T · rs749273088 · VCV288408

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 5 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00667%, sas)

Conditions

Inborn genetic diseases

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 0.13	GERP 0.34, phastCons 0.93
Overall
CADD	13.13	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00667% South Asian · 6/89,952 alleles

Filtering AF 0.00289% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00197%

Overall 0.00168% 27/1,605,914 alleles · very rare exomes 25/1,453,666 · genomes 2/152,248 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.00667%	14,992
Admixed American	0.00337%	29,676
African / African-American	0.00268%	37,366
Remaining individualsnot grpmax-eligible	0.00161%	62,184
European (non-Finnish)	0.00136%	73,412

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.Tyr90=
Coding: c.270C>T
MANE Select: NM_000337
dbSNP: rs749273088
Type: single nucleotide variant
Location: chr5:156508678 (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

Similar variants

SGCD p.Tyr90Asn 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-tyr90 (accessed [today's date]).

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