Is ABCC9 p.Asp954= (c.2862C>T) pathogenic?

ABCC9 p.Asp954= (c.2862C>T) is classified Conflicting classifications of pathogenicity in ABCC9 (ClinVar, Conflicting submitters, 8 submitters; last evaluated 2026-01-27). Low-frequency (popmax 1.06%, eas); Associated with hypertrichotic osteochondrodysplasia Cantu type.

What condition is associated with ABCC9 p.Asp954= (c.2862C>T)?

ABCC9 p.Asp954= (c.2862C>T) is associated with hypertrichotic osteochondrodysplasia Cantu type, dilated cardiomyopathy 1O (ClinVar).

How common is ABCC9 p.Asp954= (c.2862C>T) in the general population?

ABCC9 p.Asp954= (c.2862C>T) is low-frequency (popmax 1.06%, eas) (gnomAD).

ABCC9 p.Asp954=

c.2862C>T · rs2291550 · VCV45407

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 8 submitters

gnomAD v4.1

Rare

low-frequency (popmax 1.06%, eas)

Conditions

hypertrichotic osteochondrodysplasia Cantu type

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 -5.1	GERP -3.4
Overall
CADD	0.363	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 1.06% East Asian · 475/44,856 alleles

Filtering AF 0.98% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.949%

Overall 0.0348% 561/1,613,090 alleles · low-frequency

Ancestry group	Frequency	1 in
East Asiangrpmax	1.06%	94
African / African-American	0.0547%	1,828
Middle Eastern	0.0495%	2,019
Remaining individualsnot grpmax-eligible	0.032%	3,123
Admixed American	0.00834%	11,992
South Asian	0.0022%	45,529
European (non-Finnish)	0.00127%	78,618

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.Asp954=
Coding: c.2862C>T
MANE Select: NM_020297
dbSNP: rs2291550
Type: single nucleotide variant
Location: chr12:21848154 (GRCh38)
Gene constraint: LOEUF 0.557 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 81.72
Residue 954: the 'disordered' region

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

Disease context

hypertrichotic osteochondrodysplasia Cantu type — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: dilated cardiomyopathy 1O

Similar variants

ABCC9 p.Asp954Glu Uncertain significance ★ ⚠ 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
ABCC9 p.Gly989Glu 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-asp954 (accessed [today's date]).

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