CNTN3

contactin 3, the group of I-set domain containing|Contactins

Basic information

Region (hg38): 3:74262568-74614659

Previous symbols: [ "PANG" ]

Links

ENSG00000113805 ∙ NCBI:5067 ∙ OMIM:601325 ∙ HGNC:2173 ∙ Uniprot:Q9P232 ∙ 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 CNTN3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CNTN3 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				7	3	10
missense			47	10	6	63
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1	3	1	5
non coding				1	1	2
Total	0	0	47	18	10

Variants in CNTN3

This is a list of pathogenic ClinVar variants found in the CNTN3 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-74264411-A-G		not specified	Likely benign (Jul 14, 2023)
3-74264433-C-T		CNTN3-related disorder	Benign (Oct 30, 2019)
3-74264489-C-G		not specified	Uncertain significance (Sep 22, 2022)
3-74266489-C-T		not specified	Uncertain significance (Mar 07, 2024)
3-74266535-T-C		not specified	Uncertain significance (Dec 14, 2023)
3-74266571-T-C		not specified	Uncertain significance (Nov 17, 2023)
3-74266614-T-G		not specified	Uncertain significance (Oct 06, 2021)
3-74266626-T-C			Benign (Dec 31, 2019)
3-74267276-G-T		CNTN3-related disorder	Likely benign (Jan 03, 2023)
3-74267300-G-A		not specified	Uncertain significance (Jan 30, 2024)
3-74285307-G-A			Benign (Dec 31, 2019)
3-74285325-T-C		not specified	Uncertain significance (Aug 21, 2023)
3-74285465-C-T		CNTN3-related disorder	Likely benign (Aug 21, 2019)
3-74285470-C-T		not specified	Uncertain significance (Feb 13, 2024)
3-74285479-T-G		not specified	Uncertain significance (Mar 20, 2024)
3-74285487-C-T		not specified	Uncertain significance (Aug 23, 2021)
3-74295144-T-C		not specified	Uncertain significance (Feb 15, 2023)
3-74295162-T-C		not specified	Uncertain significance (Feb 23, 2023)
3-74295205-T-G		CNTN3-related disorder	Benign (Oct 30, 2019)
3-74295227-A-T		not specified	Uncertain significance (May 17, 2023)
3-74295228-C-G		not specified	Uncertain significance (Sep 14, 2022)
3-74298188-C-G		not specified	Uncertain significance (Jan 09, 2023)
3-74298196-A-G			Likely benign (May 15, 2018)
3-74299911-T-C		CNTN3-related disorder	Benign (Nov 18, 2019)
3-74301407-C-T		not specified	Uncertain significance (Dec 21, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CNTN3	protein_coding	protein_coding	ENST00000263665	22	258573

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000199	1.00	125718	0	29	125747	0.000115

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.32	460	547	0.841	0.0000275	6661
Missense in Polyphen		164	242.34	0.67673		2905
Synonymous	-0.409	207	200	1.04	0.0000106	2010
Loss of Function	4.37	18	52.0	0.346	0.00000257	649

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000213	0.000210
Ashkenazi Jewish	0.000397	0.000198
East Asian	0.0000624	0.0000544
Finnish	0.0000471	0.0000462
European (Non-Finnish)	0.000107	0.000105
Middle Eastern	0.0000624	0.0000544
South Asian	0.000198	0.000196
Other	0.000336	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Contactins mediate cell surface interactions during nervous system development. Has some neurite outgrowth-promoting activity (By similarity). {ECO:0000250}.
• Pathway: Post-translational modification: synthesis of GPI-anchored proteins;Post-translational protein modification;Metabolism of proteins (Consensus)

Recessive Scores

• pRec: 0.430

Intolerance Scores

• rvis_EVS: 0.32
• rvis_percentile_EVS: 72.8

Haploinsufficiency Scores

• pHI: 0.270
• hipred: Y
• hipred_score: 0.591
• ghis: 0.479

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.189

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cntn3

Gene ontology

• Biological process: cell adhesion;nervous system development
• Cellular component: extracellular region;plasma membrane;anchored component of membrane