CTTNBP2NL

CTTNBP2 N-terminal like, the group of STRIPAK complex

Basic information

Region (hg38): 1:112396214-112463456

Links

ENSG00000143079 ∙ NCBI:55917 ∙ OMIM:615100 ∙ HGNC:25330 ∙ Uniprot:Q9P2B4 ∙ 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 CTTNBP2NL gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CTTNBP2NL 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			31	3	2	36
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	31	3	2

Variants in CTTNBP2NL

This is a list of pathogenic ClinVar variants found in the CTTNBP2NL region.

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

Position	Type	Phenotype	Significance	ClinVar
1-112416187-A-G		not specified	Uncertain significance (Jun 10, 2024)
1-112449053-G-A			Benign (Dec 31, 2019)
1-112449086-A-G		not specified	Likely benign (Feb 23, 2023)
1-112449118-C-A		not specified	Uncertain significance (Dec 14, 2021)
1-112449122-C-A		not specified	Uncertain significance (Jul 16, 2024)
1-112454511-T-A		not specified	Uncertain significance (Dec 02, 2024)
1-112454521-A-G		not specified	Uncertain significance (Apr 25, 2022)
1-112455947-C-T		not specified	Uncertain significance (Dec 13, 2022)
1-112455989-G-A		not specified	Uncertain significance (Dec 04, 2024)
1-112456075-G-A		not specified	Uncertain significance (Nov 06, 2023)
1-112456133-T-C		not specified	Likely benign (Sep 14, 2022)
1-112456147-G-A		not specified	Uncertain significance (Mar 20, 2023)
1-112456179-G-T		not specified	Uncertain significance (Feb 21, 2024)
1-112456310-T-C		not specified	Uncertain significance (Feb 05, 2024)
1-112456324-G-A		not specified	Uncertain significance (Nov 14, 2024)
1-112456340-A-G		not specified	Uncertain significance (Mar 11, 2022)
1-112456408-A-G			Benign (Dec 31, 2019)
1-112456439-G-A		not specified	Uncertain significance (Dec 13, 2021)
1-112456457-C-T		not specified	Uncertain significance (May 31, 2023)
1-112456529-C-G		not specified	Uncertain significance (Jul 12, 2023)
1-112456544-A-C		not specified	Uncertain significance (Jul 16, 2024)
1-112456550-A-G		not specified	Uncertain significance (Jan 16, 2024)
1-112456565-C-T		not specified	Uncertain significance (Aug 20, 2024)
1-112456571-G-C		not specified	Uncertain significance (Jul 22, 2024)
1-112456594-G-T		not specified	Uncertain significance (Oct 25, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CTTNBP2NL	protein_coding	protein_coding	ENST00000271277	4	67276

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00275	0.995	125727	0	18	125745	0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.831	288	331	0.871	0.0000171	4149
Missense in Polyphen		134	165.1	0.81163		2032
Synonymous	0.477	123	130	0.947	0.00000651	1306
Loss of Function	2.64	8	21.1	0.380	0.00000114	269

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000396	0.0000396
Ashkenazi Jewish	0.00	0.00
East Asian	0.000117	0.000109
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000100	0.0000967
Middle Eastern	0.000117	0.000109
South Asian	0.000107	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.110

Intolerance Scores

• loftool: 0.621
• rvis_EVS: -0.07
• rvis_percentile_EVS: 48.69

Haploinsufficiency Scores

• pHI: 0.235
• hipred: Y
• hipred_score: 0.736
• ghis: 0.545

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.893

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cttnbp2nl

Gene ontology

• Biological process: protein dephosphorylation;negative regulation of transporter activity;negative regulation of transmembrane transport
• Cellular component: cytoplasm;actin cytoskeleton
• Molecular function: protein binding;protein phosphatase 2A binding