Is CTR9 p.Asn1157Ile (c.3470A>T) pathogenic?

CTR9 p.Asn1157Ile (c.3470A>T) is classified Benign in CTR9 (ClinVar, Single submitter, 1 submitter; last evaluated 2026-01-30). AlphaMissense: likely benign (0.1394); Rare (popmax 0.335%, sas).

How common is CTR9 p.Asn1157Ile (c.3470A>T) in the general population?

CTR9 p.Asn1157Ile (c.3470A>T) is rare (popmax 0.335%, sas) (gnomAD).

What do computational predictors say about CTR9 p.Asn1157Ile (c.3470A>T)?

AlphaMissense predicts likely benign (score 0.1394) — an in-silico prediction, not a clinical call.

CTR9 p.Asn1157Ile

c.3470A>T · rs541490334 · VCV1601071

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1394 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.335%, sas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1394	likely benign
REVEL	0.258	benign-leaning
SaProt	LLR -9.18	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 5.2	GERP 0.75, phastCons 1
Regional constraint	o/e 0.96	unconstrained · MANE · 6,491 bp · p 0.47 · regional, not allelic
Overall
CADD	24.2	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 0.335% South Asian · 305/91,082 alleles

Filtering AF 0.304% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.292%

Overall 0.0193% 312/1,614,204 alleles · rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.335%	299
Remaining individualsnot grpmax-eligible	0.0112%	8,930

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.Asn1157Ile
Coding: c.3470A>T
MANE Select: NM_014633
dbSNP: rs541490334
Type: single nucleotide variant
Location: chr11:10779053 (GRCh38)
Gene constraint: LOEUF 0.368 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 76.62 · 21 PDB
Residue 1157: the 'disordered' region

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

Similar variants

CTR9 p.Asn1157Asp Uncertain significance ★ ⚠ same residue
CTR9 p.Asn1157Thr Uncertain significance ★ ⚠ same residue
CTR9 p.Asn1157= Likely benign ★ 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

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-asn1157ile (accessed [today's date]).

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