Is ABCG1 p.Ser245= (c.735C>T) pathogenic?

ABCG1 p.Ser245= (c.735C>T) is classified Likely benign in ABCG1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-02-07). Ultra-rare (popmax 0.013%, nfe).

How common is ABCG1 p.Ser245= (c.735C>T) in the general population?

ABCG1 p.Ser245= (c.735C>T) is ultra-rare (popmax 0.013%, nfe) (gnomAD).

ABCG1 p.Ser245=

c.735C>T · VCV3883554

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.013%, nfe)

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 -8	GERP -4.1
Overall
CADD	7.759	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.013% European (non-Finnish) · 153/1,179,948 alleles

Filtering AF 0.0113% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0107%

Overall 0.0101% 163/1,612,664 alleles · ultra-rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.013%	7,712
African / African-American	0.00934%	10,705
Remaining individualsnot grpmax-eligible	0.0032%	31,234
Finnishnot grpmax-eligible	0.00159%	62,752

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: ABCG1
Protein: p.Ser245=
Coding: c.735C>T
MANE Select: NM_016818
Type: single nucleotide variant
Location: chr21:42284560 (GRCh38)
Gene constraint: LOEUF 0.573 · pLI 0.20 (gnomAD)
Structure: AlphaFold pLDDT 81.34 · 5 PDB
Residue 245: the abc transporter domain; a β-strand

Full ABCG1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ABCG1 p.Ser245Arg Uncertain significance ★ ⚠ same residue
ABCG1 p.Ala456= Benign ★★ same type
ABCG1 p.Leu643= Likely benign ★★ same type
ABCG1 p.Pro149= Benign ★★ same type
ABCG1 p.Ser547= Benign ★★ same type
ABCG1 c.1122+21A>C Uncertain significance ★ ⚠ same type
ABCG1 c.1122+24G>C Uncertain significance ★ ⚠ same type
ABCG1 c.1122+2T>C Uncertain significance ★ ⚠ same type

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/abcg1-p-ser245 (accessed [today's date]).

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