Is AKAP9 p.Ala2012= (c.6036T>G) pathogenic?

AKAP9 p.Ala2012= (c.6036T>G) is classified Likely benign in AKAP9 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-01-14). Absent from gnomAD v4.1; Associated with Cardiovascular phenotype.

What condition is associated with AKAP9 p.Ala2012= (c.6036T>G)?

AKAP9 p.Ala2012= (c.6036T>G) is associated with Cardiovascular phenotype (ClinVar).

How common is AKAP9 p.Ala2012= (c.6036T>G) in the general population?

AKAP9 p.Ala2012= (c.6036T>G) is absent from gnomAD v4.1 (gnomAD).

AKAP9 p.Ala2012=

c.6036T>G · rs2535203699 · VCV3225077

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

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 -0.21	GERP 0.2, phastCons 0.45
Overall
CADD	6.676	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: AKAP9
Protein: p.Ala2012=
Coding: c.6036T>G
MANE Select: NM_005751
dbSNP: rs2535203699
Type: single nucleotide variant
Location: chr7:92065289 (GRCh38)
Gene constraint: LOEUF 0.662 · pLI <0.01 (gnomAD)

Full AKAP9 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

AKAP9 p.Ala2012Gly Uncertain significance ★★ ⚠ same residue
AKAP9 c.11687-2A>G Uncertain significance ★★ same condition
AKAP9 c.3953-3T>C Uncertain significance ★★ same condition
AKAP9 c.5058+2T>C Uncertain significance ★★ same condition
AKAP9 c.5162+3A>G Uncertain significance ★★ same condition
AKAP9 c.5162+4T>A Uncertain significance ★★ same condition
AKAP9 c.5162+5A>G Uncertain significance ★★ same condition
AKAP9 c.5601+4A>C 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/akap9-p-ala2012 (accessed [today's date]).

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