CD2BP2

CD2 cytoplasmic tail binding protein 2, the group of U5 small nuclear ribonucleoprotein|Protein phosphatase 1 regulatory subunits

Basic information

Region (hg38): 16:30350773-30355308

Links

ENSG00000169217 ∙ NCBI:10421 ∙ OMIM:604470 ∙ HGNC:1656 ∙ Uniprot:O95400 ∙ 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 CD2BP2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CD2BP2 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			22			22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	0	0

Variants in CD2BP2

This is a list of pathogenic ClinVar variants found in the CD2BP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-30353016-G-C		not specified	Uncertain significance (Nov 17, 2022)
16-30353044-C-A		not specified	Uncertain significance (May 21, 2024)
16-30353197-G-A		not specified	Uncertain significance (Jan 06, 2023)
16-30353201-A-C		not specified	Uncertain significance (Apr 07, 2022)
16-30353273-C-T		not specified	Uncertain significance (Sep 27, 2021)
16-30353278-G-A		not specified	Uncertain significance (Oct 26, 2022)
16-30353409-G-A		not specified	Uncertain significance (Mar 06, 2023)
16-30353461-G-C		not specified	Uncertain significance (Jan 09, 2024)
16-30353491-G-C		not specified	Uncertain significance (Apr 06, 2024)
16-30353494-G-A		not specified	Uncertain significance (Oct 22, 2021)
16-30353502-A-C		not specified	Uncertain significance (Jan 17, 2024)
16-30353568-G-A		not specified	Uncertain significance (Apr 06, 2024)
16-30353575-G-A		not specified	Uncertain significance (Dec 06, 2022)
16-30353616-C-T		not specified	Uncertain significance (May 02, 2024)
16-30353647-G-C		not specified	Uncertain significance (Dec 16, 2022)
16-30353686-G-A		not specified	Uncertain significance (Mar 27, 2023)
16-30353706-A-G		not specified	Uncertain significance (May 23, 2024)
16-30353744-C-A		not specified	Uncertain significance (Apr 18, 2023)
16-30353754-G-A		not specified	Uncertain significance (Apr 25, 2022)
16-30353790-C-T		not specified	Uncertain significance (Aug 02, 2022)
16-30353915-C-A		not specified	Uncertain significance (Jul 13, 2021)
16-30354017-T-C		not specified	Uncertain significance (Feb 16, 2023)
16-30354020-G-A		not specified	Uncertain significance (Apr 19, 2023)
16-30354201-G-A		not specified	Uncertain significance (Apr 09, 2024)
16-30354238-C-G		not specified	Uncertain significance (Apr 25, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CD2BP2	protein_coding	protein_coding	ENST00000305596	6	4596

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000152	0.870	125713	0	35	125748	0.000139

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.559	233	210	1.11	0.0000129	2209
Missense in Polyphen		53	55.736	0.95091		644
Synonymous	-2.88	117	83.5	1.40	0.00000486	680
Loss of Function	1.46	10	16.4	0.612	8.70e-7	184

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000291	0.0000291
Ashkenazi Jewish	0.00	0.00
East Asian	0.000273	0.000272
Finnish	0.000323	0.000323
European (Non-Finnish)	0.000141	0.000141
Middle Eastern	0.000273	0.000272
South Asian	0.000163	0.000163
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in pre-mRNA splicing as component of the U5 snRNP complex that is involved in spliceosome assembly. {ECO:0000269|PubMed:15840814}.
• Pathway: mRNA Processing;Metabolism of RNA;mRNA Splicing - Major Pathway;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA (Consensus)

Recessive Scores

• pRec: 0.125

Intolerance Scores

• loftool: 0.597
• rvis_EVS: 0.06
• rvis_percentile_EVS: 58.74

Haploinsufficiency Scores

• pHI: 0.334
• hipred: Y
• hipred_score: 0.595
• ghis: 0.499

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.668

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cd2bp2

Gene ontology

• Biological process: spliceosomal tri-snRNP complex assembly;mRNA splicing, via spliceosome;negative regulation of phosphatase activity
• Cellular component: fibrillar center;nucleus;nucleoplasm;U5 snRNP;cytoplasm;cytosol;nuclear speck;U4/U6 x U5 tri-snRNP complex
• Molecular function: protein binding;ribonucleoprotein complex binding