Is ABCC9 p.Asn16= (c.48C>T) pathogenic?

ABCC9 p.Asn16= (c.48C>T) is classified Likely benign in ABCC9 (ClinVar, Multiple submitters, 7 submitters; last evaluated 2025-11-24). Ultra-rare (popmax 0.0329%, mid); Associated with Cardiovascular phenotype.

What condition is associated with ABCC9 p.Asn16= (c.48C>T)?

ABCC9 p.Asn16= (c.48C>T) is associated with Cardiovascular phenotype, dilated cardiomyopathy 1O (ClinVar).

How common is ABCC9 p.Asn16= (c.48C>T) in the general population?

ABCC9 p.Asn16= (c.48C>T) is ultra-rare (popmax 0.0329%, mid) (gnomAD).

ABCC9 p.Asn16=

c.48C>T · rs199631710 · VCV162699

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 7 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0329%, mid)

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 -2	GERP -3.8
Overall
CADD	0.603	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0329% Middle Eastern · 2/6,076 alleles

Filtering AF 0.00581% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00515%

Overall 0.00608% 98/1,610,814 alleles · ultra-rare

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0329%	3,038
Remaining individualsnot grpmax-eligible	0.00802%	12,476
European (non-Finnish)	0.0068%	14,717
African / African-American	0.00668%	14,964
East Asian	0.00446%	22,418
Admixed American	0.00334%	29,968
South Asian	0.0022%	45,484

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.Asn16=
Coding: c.48C>T
MANE Select: NM_020297
dbSNP: rs199631710
Type: single nucleotide variant
Location: chr12:21936627 (GRCh38)
Gene constraint: LOEUF 0.557 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 81.72

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

Also linked: dilated cardiomyopathy 1O

Similar variants

ABCC9 p.Asn16Lys Uncertain significance ★ ⚠ same residue
ABCC9 p.Asn16Ser Conflicting classifications of pathogenicity ★ ⚠ same residue
ABCC9 c.2506-1G>A Pathogenic/Likely pathogenic ★★ same condition
ABCC9 p.Arg1116Cys Pathogenic/Likely pathogenic ★★ ⚠ same condition
ABCC9 p.Arg1116His Pathogenic ★★ ⚠ same condition
ABCC9 p.Arg1154Gln Pathogenic ★★ same condition
ABCC9 p.Arg1154Trp Pathogenic/Likely pathogenic ★★ same condition
ABCC9 p.Gln852Ter Pathogenic/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/abcc9-p-asn16 (accessed [today's date]).

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