CTXN2

cortexin 2

Basic information

Region (hg38): 15:48178122-48203758

Links

ENSG00000233932 ∙ NCBI:399697 ∙ ∙ HGNC:31109 ∙ Uniprot:P0C2S0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CTXN2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CTXN2 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			3			3
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			5	1		6
Total	0	0	8	1	0

Variants in CTXN2

This is a list of pathogenic ClinVar variants found in the CTXN2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
15-48178132-C-G		not specified	Likely benign (May 06, 2022)
15-48178134-G-T		not specified	Uncertain significance (Sep 20, 2023)
15-48178165-G-T		not specified	Uncertain significance (Apr 18, 2023)
15-48178181-G-C		not specified	Uncertain significance (Dec 20, 2023)
15-48178210-G-A		not specified	Uncertain significance (Aug 28, 2023)
15-48178216-C-T		not specified	Uncertain significance (Apr 20, 2023)
15-48201395-C-A		not specified	Uncertain significance (Jul 14, 2021)
15-48201415-A-G		not specified	Uncertain significance (Jan 23, 2023)
15-48201541-G-A		not specified	Uncertain significance (Sep 15, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CTXN2	protein_coding	protein_coding	ENST00000417307	1	12218

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0352	0.641	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.977	24	41.8	0.575	0.00000199	528
Missense in Polyphen		15	23.147	0.64804		288
Synonymous	0.649	14	17.4	0.802	0.00000102	155
Loss of Function	0.350	2	2.61	0.766	1.95e-7	28

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 0.35
• rvis_percentile_EVS: 73.79

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.231

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Ctxn2

Gene ontology

• Cellular component: integral component of membrane