Is CTR9 p.Lys956fs (c.2867_2870del) pathogenic?

CTR9 p.Lys956fs (c.28672870del) is classified Uncertain significance in CTR9 (ClinVar, Single submitter, 1 submitter; last evaluated 2019-09-08). No gnomAD frequency available for this variant.

How common is CTR9 p.Lys956fs (c.2867_2870del) in the general population?

CTR9 p.Lys956fs (c.2867_2870del) is no gnomAD frequency available for this variant (gnomAD).

CTR9 p.Lys956fs

c.2867_2870del · rs1863191798 · VCV956344

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a LoF-intolerant gene
NMD	predicted	premature termination codon in exon 22 of 25
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 1.3	GERP -3.2, phastCons 1
Region caveats
Repeat context	tandem	GA-rich low complexity · ambiguous alignment · confidence, not pathogenicity

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: CTR9
Protein: p.Lys956fs
Coding: c.2867_2870del
MANE Select: NM_014633
dbSNP: rs1863191798
Type: Microsatellite
Location: chr11:10774147 (GRCh38)
Gene constraint: LOEUF 0.368 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 76.62 · 21 PDB
Residue 956: the 'disordered' region

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

Similar variants

CTR9 p.Arg962del Uncertain significance ★ same type
CTR9 p.Glu100_Lys101insTer Uncertain significance ★ same type
CTR9 p.Glu968del Uncertain significance ★ same type
CTR9 c.1687-139AAAG[2] Likely benign ★ same type
CTR9 c.2227-15_2227-12del Likely benign ★ same type
CTR9 c.3095+104_3095+109del Benign ★ same type
CTR9 c.592+19_592+23del Likely benign ★ 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-lys956fs (accessed [today's date]).

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