Is AKAP9 p.Ser891= (c.2673T>C) pathogenic?

AKAP9 p.Ser891= (c.2673T>C) is classified Likely benign in AKAP9 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-04-07). Ultra-rare (popmax 0.0151%, amr); Associated with Cardiovascular phenotype.

What condition is associated with AKAP9 p.Ser891= (c.2673T>C)?

AKAP9 p.Ser891= (c.2673T>C) is associated with Cardiovascular phenotype, long QT syndrome (ClinVar).

How common is AKAP9 p.Ser891= (c.2673T>C) in the general population?

AKAP9 p.Ser891= (c.2673T>C) is ultra-rare (popmax 0.0151%, amr) (gnomAD).

AKAP9 p.Ser891=

c.2673T>C · rs200821358 · VCV2158012

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0151%, amr)

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 0.038	GERP 1.1, phastCons 0.15
Overall
CADD	6.484	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0151% Admixed American · 9/59,502 alleles

Filtering AF 0.00779% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00583%

Overall 0.000559% 9/1,610,148 alleles · ultra-rare

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: AKAP9
Protein: p.Ser891=
Coding: c.2673T>C
MANE Select: NM_005751
dbSNP: rs200821358
Type: single nucleotide variant
Location: chr7:92002590 (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

Also linked: long QT syndrome

Similar variants

AKAP9 c.10713+4A>G Uncertain significance ★★ same condition
AKAP9 c.11686+4C>T Uncertain significance ★★ same condition
AKAP9 c.11687-2A>G Uncertain significance ★★ same condition
AKAP9 c.3838-4A>G Uncertain significance ★★ same condition
AKAP9 c.3953-3T>C Uncertain significance ★★ same condition
AKAP9 c.405+3A>G Uncertain significance ★★ same condition
AKAP9 c.48+5G>A Uncertain significance ★★ same condition
AKAP9 c.49-3T>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-ser891 (accessed [today's date]).

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