BCCIP

BRCA2 and CDKN1A interacting protein

Basic information

Region (hg38): 10:125823545-125853695

Links

ENSG00000107949 ∙ NCBI:56647 ∙ OMIM:611883 ∙ HGNC:978 ∙ Uniprot:Q9P287 ∙ 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 BCCIP gene.

• not provided (156 variants)
• Inborn genetic diseases (29 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BCCIP 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			9	2		11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			102	58	6	166
Total	0	0	111	60	6

Variants in BCCIP

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

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

Position	Type	Phenotype	Significance	ClinVar
10-125823567-A-G		not specified	Uncertain significance (Sep 27, 2021)
10-125823570-T-C		not specified	Likely benign (May 11, 2022)
10-125823589-A-G		not specified	Likely benign (Sep 28, 2022)
10-125823632-C-G		not specified	Uncertain significance (Jan 10, 2023)
10-125823645-A-G		not specified	Uncertain significance (Oct 26, 2022)
10-125823675-G-A		not specified	Uncertain significance (Jan 23, 2024)
10-125826598-A-G		not specified	Uncertain significance (Nov 07, 2022)
10-125827619-A-G		not specified	Uncertain significance (Feb 27, 2024)
10-125831460-G-A		not specified	Uncertain significance (Jul 28, 2021)
10-125833792-A-C		not specified	Uncertain significance (Jan 03, 2022)
10-125833892-C-G		not specified	Uncertain significance (Aug 21, 2023)
10-125833905-G-A		not specified	Uncertain significance (Feb 13, 2023)
10-125833906-C-T		not specified	Uncertain significance (Nov 15, 2021)
10-125836697-G-T		not specified	Uncertain significance (Jan 23, 2024)
10-125836701-A-T			Uncertain significance (Feb 21, 2023)
10-125836702-T-C			Likely benign (Jul 25, 2022)
10-125836702-TC-GA			Uncertain significance (Jan 09, 2024)
10-125836710-C-G		not specified	Uncertain significance (Jan 15, 2024)
10-125836723-C-T			Likely benign (Sep 26, 2022)
10-125836724-G-A			Uncertain significance (Mar 18, 2023)
10-125836726-C-A			Uncertain significance (Jul 03, 2023)
10-125836727-T-A			Uncertain significance (Jun 11, 2022)
10-125836728-C-G			Uncertain significance (Dec 11, 2023)
10-125836730-C-A			Uncertain significance (Oct 18, 2022)
10-125836732-C-T			Uncertain significance (Mar 04, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BCCIP	protein_coding	protein_coding	ENST00000368759	8	30150

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00785	0.979	125676	0	72	125748	0.000286

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0989	175	171	1.02	0.00000823	2133
Missense in Polyphen		19	31.426	0.60459		430
Synonymous	0.416	62	66.3	0.935	0.00000342	589
Loss of Function	2.17	6	15.1	0.397	6.38e-7	198

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000370	0.000304
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.0000469	0.0000462
European (Non-Finnish)	0.000533	0.000519
Middle Eastern	0.000163	0.000163
South Asian	0.0000704	0.0000653
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: During interphase, required for microtubule organizing and anchoring activities. During mitosis, required for the organization and stabilization of the spindle pole (PubMed:28394342). Isoform 2/alpha is particularly important for the regulation of microtubule anchoring, microtubule stability, spindle architecture and spindle orientation, compared to isoform 1/beta (PubMed:28394342). May promote cell cycle arrest by enhancing the inhibition of CDK2 activity by CDKN1A. May be required for repair of DNA damage by homologous recombination in conjunction with BRCA2. May not be involved in non-homologous end joining (NHEJ). {ECO:0000269|PubMed:10878006, ECO:0000269|PubMed:14726710, ECO:0000269|PubMed:15539944, ECO:0000269|PubMed:15713648, ECO:0000269|PubMed:17947333, ECO:0000269|PubMed:28394342}.

Recessive Scores

• pRec: 0.0887

Intolerance Scores

• loftool: 0.917
• rvis_EVS: -0.71
• rvis_percentile_EVS: 14.4

Haploinsufficiency Scores

• pHI: 0.311
• hipred: Y
• hipred_score: 0.624
• ghis: 0.635

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0207

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Bccip

Gene ontology

• Biological process: ribosomal large subunit export from nucleus;regulation of cyclin-dependent protein serine/threonine kinase activity;establishment of mitotic spindle orientation;microtubule cytoskeleton organization;DNA repair;cellular response to DNA damage stimulus;mitotic spindle organization;microtubule anchoring;neuroendocrine cell differentiation;mitotic spindle assembly
• Cellular component: nucleus;nucleoplasm;centrosome;centriole;cytosol;nuclear cyclin-dependent protein kinase holoenzyme complex;mitotic spindle pole
• Molecular function: RNA binding;protein binding;tubulin binding;kinase regulator activity