Is CTR9 p.Glu15Lys (c.43G>A) pathogenic?

CTR9 p.Glu15Lys (c.43G>A) is classified Likely pathogenic in CTR9 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-04-01). AlphaMissense: likely pathogenic (0.9995); Absent from gnomAD v4.1; Associated with CTR9-related neurodevelopmental disorder.

What condition is associated with CTR9 p.Glu15Lys (c.43G>A)?

CTR9 p.Glu15Lys (c.43G>A) is associated with CTR9-related neurodevelopmental disorder (ClinVar).

How common is CTR9 p.Glu15Lys (c.43G>A) in the general population?

CTR9 p.Glu15Lys (c.43G>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CTR9 p.Glu15Lys (c.43G>A)?

AlphaMissense predicts likely pathogenic (score 0.9995) — an in-silico prediction, not a clinical call.

CTR9 p.Glu15Lys

c.43G>A · rs2135351445 · VCV1173018

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9995 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

2/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

CTR9-related neurodevelopmental disorder

Computational evidence

Protein change
AlphaMissense	0.9995	likely pathogenic ✓ concordant with ClinVar · top 4% in CTR9
REVEL	0.534	indeterminate
SaProt	LLR -12.11	damaging
⇒ AlphaMissense and SaProt both call this damaging; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 2, phastCons 1
Regional constraint	o/e 0.29	constrained · MANE · 1,327 bp · p 6.7e-07 · regional, not allelic
Overall
CADD	34.0	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

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: CTR9
Protein: p.Glu15Lys
Coding: c.43G>A
MANE Select: NM_014633
dbSNP: rs2135351445
Type: single nucleotide variant
Location: chr11:10751455 (GRCh38)
Gene constraint: LOEUF 0.368 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 76.62 · 21 PDB

Full CTR9 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

CTR9-related neurodevelopmental disorder — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CTR9 p.Glu15Gly Likely pathogenic ★ same residue
CTR9 p.Glu15= Uncertain significance ★ same residue
CTR9 p.Asn455Ser Likely pathogenic ★★ same condition
CTR9 p.Ile17Thr Pathogenic/Likely pathogenic ★★ same condition
CTR9 p.Pro25Arg Pathogenic/Likely pathogenic ★★ same condition
CTR9 c.46-1G>T Pathogenic ★ same condition
CTR9 p.Arg878Gln Likely pathogenic ★ ⚠ same condition
CTR9 p.Cys85Tyr 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/ctr9-p-glu15lys (accessed [today's date]).

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