CTXN1

cortexin 1

Basic information

Region (hg38): 19:7924491-7926135

Links

ENSG00000178531 ∙ NCBI:404217 ∙ OMIM:600135 ∙ HGNC:31108 ∙ Uniprot:P60606 ∙ 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 CTXN1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CTXN1 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			5			5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	5	0	0

Variants in CTXN1

This is a list of pathogenic ClinVar variants found in the CTXN1 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-7925359-C-T		not specified	Uncertain significance (May 23, 2023)
19-7925372-G-A		not specified	Uncertain significance (Dec 16, 2023)
19-7925414-A-G		not specified	Uncertain significance (Nov 10, 2022)
19-7925462-G-A		not specified	Uncertain significance (Mar 14, 2023)
19-7925472-C-T		not specified	Uncertain significance (Apr 27, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CTXN1	protein_coding	protein_coding	ENST00000318978	1	1680

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.411	0.476	102516	0	1	102517	0.00000488

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.46	16	42.8	0.374	0.00000196	500
Missense in Polyphen		9	21.524	0.41813		246
Synonymous	0.255	20	21.5	0.930	0.00000101	176
Loss of Function	0.997	0	1.16	0.00	4.99e-8	13

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000697	0.0000697
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.0000697	0.0000697
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May mediate extracellular or intracellular signaling of cortical neurons during forebrain development. {ECO:0000250}.

Recessive Scores

• pRec: 0.113

Haploinsufficiency Scores

• pHI: 0.207
• hipred: Y
• hipred_score: 0.546
• ghis: 0.613

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: Ctxn1

Gene ontology

• Cellular component: integral component of membrane