Is CTR9 p.Glu951Asp (c.2853G>C) pathogenic?

CTR9 p.Glu951Asp (c.2853G>C) is classified Benign in CTR9 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-08-25). AlphaMissense: likely benign (0.0607); Rare (popmax 0.362%, sas).

How common is CTR9 p.Glu951Asp (c.2853G>C) in the general population?

CTR9 p.Glu951Asp (c.2853G>C) is rare (popmax 0.362%, sas) (gnomAD).

What do computational predictors say about CTR9 p.Glu951Asp (c.2853G>C)?

AlphaMissense predicts likely benign (score 0.0607) — an in-silico prediction, not a clinical call.

CTR9 p.Glu951Asp

c.2853G>C · rs568774868 · VCV1169846

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0607 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.362%, sas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0607	likely benign
REVEL	0.04	moderately benign-leaning
SaProt	LLR -7.19	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.48	GERP -1.9, phastCons 0.98
Regional constraint	o/e 0.96	unconstrained · MANE · 6,491 bp · p 0.47 · regional, not allelic
Overall
CADD	12.03	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

Grpmax group 0.362% South Asian · 328/90,506 alleles

Filtering AF 0.33% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.317%

Overall 0.0215% 344/1,603,634 alleles · rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.362%	276
Middle Eastern	0.0497%	2,012
Remaining individualsnot grpmax-eligible	0.0113%	8,876
African / African-American	0.00268%	37,329
European (non-Finnish)	0.000341%	292,916

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: CTR9
Protein: p.Glu951Asp
Coding: c.2853G>C
MANE Select: NM_014633
dbSNP: rs568774868
Type: single nucleotide variant
Location: chr11:10774137 (GRCh38)
Gene constraint: LOEUF 0.368 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 76.62 · 21 PDB
Residue 951: the 'disordered' region

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

Similar variants

CTR9 p.Glu951Lys Uncertain significance ★ ⚠ same residue
CTR9 p.Asn455Ser Likely pathogenic ★★ same type
CTR9 p.Ile17Thr Pathogenic/Likely pathogenic ★★ same type
CTR9 p.Pro25Arg Pathogenic/Likely pathogenic ★★ same type
CTR9 c.1960+3G>A Uncertain significance ★★ same type
CTR9 c.2109+4A>G Uncertain significance ★★ same type
CTR9 c.2445-3T>C Uncertain significance ★★ same type
CTR9 c.45+5G>T Uncertain significance ★★ same type

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-glu951asp (accessed [today's date]).

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