Is ABCC9 p.Ser1006= (c.3018G>C) pathogenic?

ABCC9 p.Ser1006= (c.3018G>C) is classified Likely benign in ABCC9 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-11-16). Very rare (popmax 0.00879%, sas); Associated with Cardiovascular phenotype.

What condition is associated with ABCC9 p.Ser1006= (c.3018G>C)?

ABCC9 p.Ser1006= (c.3018G>C) is associated with Cardiovascular phenotype (ClinVar).

How common is ABCC9 p.Ser1006= (c.3018G>C) in the general population?

ABCC9 p.Ser1006= (c.3018G>C) is very rare (popmax 0.00879%, sas) (gnomAD).

ABCC9 p.Ser1006=

c.3018G>C · VCV4613318

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00879%, sas)

Conditions

Cardiovascular phenotype

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 -8.7	GERP -3.7
Overall
CADD	0.283	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00879% South Asian · 8/91,062 alleles

Filtering AF 0.00437% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00312%

Overall 0.000616% 9/1,461,616 alleles · very rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.00879%	11,383
East Asian	0.00223%	44,858

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: ABCC9
Protein: p.Ser1006=
Coding: c.3018G>C
MANE Select: NM_020297
Type: single nucleotide variant
Location: chr12:21845681 (GRCh38)
Gene constraint: LOEUF 0.557 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 81.72
Residue 1006: the abc transmembrane type-1 2 domain

Full ABCC9 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Cardiovascular phenotype — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

ABCC9 c.2092+5G>T Uncertain significance ★★ same condition
ABCC9 c.3893-3C>T Uncertain significance ★★ same condition
ABCC9 c.4512+693G>A Uncertain significance ★★ ⚠ same condition
ABCC9 c.4512+733C>A Uncertain significance ★★ ⚠ same condition
ABCC9 p.Ala136Ser Uncertain significance ★★ same condition
ABCC9 p.Ala276Thr Uncertain significance ★★ ⚠ same condition
ABCC9 p.Ala351Ser Uncertain significance ★★ ⚠ same condition
ABCC9 p.Ala461Pro 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/abcc9-p-ser1006 (accessed [today's date]).

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