Is SGCD p.Pro88= (c.264T>A) pathogenic?

SGCD p.Pro88= (c.264T>A) is classified Likely benign in SGCD (ClinVar, Single submitter, 1 submitter; last evaluated 2024-02-04). Very rare (popmax 0.00134%, afr); Associated with Inborn genetic diseases.

What condition is associated with SGCD p.Pro88= (c.264T>A)?

SGCD p.Pro88= (c.264T>A) is associated with Inborn genetic diseases (ClinVar).

How common is SGCD p.Pro88= (c.264T>A) in the general population?

SGCD p.Pro88= (c.264T>A) is very rare (popmax 0.00134%, afr) (gnomAD).

SGCD p.Pro88=

c.264T>A · rs201071631 · VCV3231257

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00134%, afr)

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 2.3	GERP -4, phastCons 1
Overall
CADD	9.304	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00134% African / African-American · 1/74,840 alleles

Overall 6.22e-05% 1/1,608,778 alleles · very rare exomes 0/1,456,536 · genomes 1/152,242 · joint denominator

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.Pro88=
Coding: c.264T>A
MANE Select: NM_000337
dbSNP: rs201071631
Type: single nucleotide variant
Location: chr5:156508672 (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

Similar variants

SGCD p.Pro88Ser Uncertain significance ★ ⚠ same residue
SGCD p.Ala134Val Uncertain significance ★★ ⚠ same condition
SGCD p.Ala267Thr Uncertain significance ★★ ⚠ same condition
SGCD p.Arg11Trp Uncertain significance ★★ ⚠ same condition
SGCD p.Arg198Gln Uncertain significance ★★ ⚠ same condition
SGCD p.Arg270Lys Uncertain significance ★★ ⚠ same condition
SGCD p.Arg33Gln Uncertain significance ★★ ⚠ same condition
SGCD p.Asn268Ser Uncertain significance ★★ ⚠ 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-pro88 (accessed [today's date]).

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