CNTNAP3B

contactin associated protein family member 3B, the group of Contactin associated protein family

Basic information

Region (hg38): 9:41890314-42129510

Links

ENSG00000154529 ∙ NCBI:728577 ∙ ∙ HGNC:32035 ∙ Uniprot:Q96NU0 ∙ 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 CNTNAP3B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CNTNAP3B 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				2	1	3
missense			115	12		127
nonsense						0
start loss						0
frameshift					1	1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	115	14	3

Variants in CNTNAP3B

This is a list of pathogenic ClinVar variants found in the CNTNAP3B region.

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

Position	Type	Phenotype	Significance	ClinVar
9-41893993-C-A		not specified	Uncertain significance (Nov 08, 2022)
9-41893994-A-G		not specified	Uncertain significance (Feb 13, 2024)
9-41894003-T-C		not specified	Uncertain significance (Dec 28, 2023)
9-41894033-G-A		not specified	Uncertain significance (Jul 06, 2021)
9-41894038-T-A		not specified	Uncertain significance (Sep 17, 2021)
9-41894045-G-T		not specified	Uncertain significance (Jun 22, 2021)
9-41894056-C-T		not specified	Uncertain significance (Aug 12, 2021)
9-41894057-G-A		not specified	Uncertain significance (Oct 27, 2023)
9-41894062-G-T		not specified	Uncertain significance (Mar 07, 2023)
9-41894102-C-T		not specified	Uncertain significance (Dec 26, 2023)
9-41898476-G-T		not specified	Uncertain significance (Mar 30, 2024)
9-41898518-A-G		not specified	Likely benign (Dec 27, 2022)
9-41898793-C-A		not specified	Uncertain significance (Mar 22, 2023)
9-41898807-G-C		not specified	Uncertain significance (Jun 09, 2022)
9-41898819-G-A		not specified	Likely benign (Jun 30, 2022)
9-41898832-C-T		not specified	Uncertain significance (Dec 18, 2023)
9-41898846-G-A		not specified	Uncertain significance (Jan 09, 2024)
9-41898853-C-G		not specified	Uncertain significance (Aug 17, 2022)
9-41898883-C-G		not specified	Uncertain significance (Apr 08, 2024)
9-41898885-C-T		not specified	Uncertain significance (Oct 12, 2021)
9-41898888-G-A		not specified	Uncertain significance (Mar 01, 2024)
9-41898898-C-T		not specified	Uncertain significance (Jul 06, 2021)
9-41898902-C-A		not specified	Uncertain significance (Aug 10, 2021)
9-41898934-C-T		not specified	Uncertain significance (Dec 28, 2022)
9-41898963-G-A		not specified	Likely benign (May 11, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CNTNAP3B	protein_coding	protein_coding	ENST00000377564	24	239148

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.59e-29	0.00000403	125459	2	53	125514	0.000219

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-2.48	423	302	1.40	0.0000161	8020
Missense in Polyphen		107	75.159	1.4236		2149
Synonymous	-2.49	162	126	1.28	0.00000768	2512
Loss of Function	-1.39	38	29.8	1.27	0.00000163	699

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000879	0.000774
Ashkenazi Jewish	0.00	0.00
East Asian	0.000241	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000202	0.000176
Middle Eastern	0.000241	0.000163
South Asian	0.000650	0.000490
Other	0.000210	0.000163

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• pHI: 0.170

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.154

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Gene ontology

• Biological process: cell adhesion
• Cellular component: integral component of membrane