CTXN3

cortexin 3

Basic information

Region (hg38): 5:127649082-127658630

Links

ENSG00000205279 ∙ NCBI:613212 ∙ OMIM:618746 ∙ HGNC:31110 ∙ Uniprot:Q4LDR2 ∙ 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 CTXN3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CTXN3 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			4			4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	4	0	0

Variants in CTXN3

This is a list of pathogenic ClinVar variants found in the CTXN3 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-127657558-C-A		not specified	Uncertain significance (Jan 22, 2024)
5-127657660-C-T		not specified	Uncertain significance (Apr 18, 2023)
5-127657698-G-C		not specified	Uncertain significance (Mar 20, 2023)
5-127657703-C-A		not specified	Uncertain significance (May 13, 2024)
5-127657709-C-T		not specified	Uncertain significance (Dec 04, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CTXN3	protein_coding	protein_coding	ENST00000379445	1	9587

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.140	0.640	125734	0	6	125740	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.195	41	44.7	0.918	0.00000244	518
Missense in Polyphen		20	23.636	0.84618		283
Synonymous	-0.567	21	17.9	1.17	9.42e-7	172
Loss of Function	0.602	1	1.89	0.528	1.46e-7	18

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000867	0.0000867
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0975

Intolerance Scores

• rvis_EVS: 0.44
• rvis_percentile_EVS: 77.45

Haploinsufficiency Scores

• pHI: 0.613
• hipred: N
• hipred_score: 0.366

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0862

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ctxn3

Gene ontology

• Cellular component: integral component of membrane