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.

• not_specified (279 variants)
• not_provided (10 variants)

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. These statistics are base on transcript: NM_001201380.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				3	1	4
missense			263	18		281
nonsense						0
start loss						0
frameshift					1	1
splice donor/acceptor (+/-2bp)						0
Total	0	0	263	21	2

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