Is ABCG5 p.Ser23= (c.69C>T) pathogenic?

ABCG5 p.Ser23= (c.69C>T) is classified Uncertain significance in ABCG5 (ClinVar, Single submitter, 1 submitter; last evaluated 2018-01-13). Absent from gnomAD v4.1; Associated with sitosterolemia 1.

What condition is associated with ABCG5 p.Ser23= (c.69C>T)?

ABCG5 p.Ser23= (c.69C>T) is associated with sitosterolemia 1 (ClinVar).

How common is ABCG5 p.Ser23= (c.69C>T) in the general population?

ABCG5 p.Ser23= (c.69C>T) is absent from gnomAD v4.1 (gnomAD).

How is Sitosterolemia inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

ABCG5 p.Ser23=

c.69C>T · rs1668435419 · VCV895031

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

sitosterolemia 1

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 1.1	GERP -3.2, phastCons 0.001
Overall
CADD	7.106	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: ABCG5
Protein: p.Ser23=
Coding: c.69C>T
MANE Select: NM_022436
dbSNP: rs1668435419
Type: single nucleotide variant
Location: chr2:43838611 (GRCh38)
Gene constraint: LOEUF 1.219 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 85.48 · 8 PDB
Residue 23: the 'disordered' region

Full ABCG5 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

sitosterolemia 1 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Sitosterolemia (Orphanet):

Inheritance: Autosomal recessive
Onset: All ages

Similar variants

ABCG5 p.Ser23Asn Uncertain significance ★ ⚠ same residue
ABCG5 p.Arg446Ter Pathogenic/Likely pathogenic ★★ same condition
ABCG5 p.Glu26Asp Uncertain significance ★★ ⚠ same condition
ABCG5 p.Gly79Arg Uncertain significance ★★ ⚠ same condition
ABCG5 p.Leu625Val Uncertain significance ★★ ⚠ same condition
ABCG5 p.Phe300Leu Uncertain significance ★★ ⚠ same condition
ABCG5 p.Phe399Cys Uncertain significance ★★ same condition
ABCG5 p.Phe624Leu 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/abcg5-p-ser23 (accessed [today's date]).

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