BICC1

BicC family RNA binding protein 1, the group of Sterile alpha motif domain containing

Basic information

Region (hg38): 10:58512872-58831435

Links

ENSG00000122870 ∙ NCBI:80114 ∙ OMIM:614295 ∙ HGNC:19351 ∙ Uniprot:Q9H694 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• renal dysplasia, cystic, susceptibility to (Limited), mode of inheritance: Unknown
• renal dysplasia, cystic, susceptibility to (Limited), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Renal dysplasia, cystic, susceptibility to	AD	Renal	Sequelae can include vesicoureteral reflux, and early diagnosis could be helpful to institute measures to preserve kidney function	Renal	21922595

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the BICC1 gene.

• Renal dysplasia, cystic, susceptibility to (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BICC1 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	33	2	37
missense			92	8	7	107
nonsense		1	2			3
start loss						0
frameshift	1	2				3
inframe indel						0
splice donor/acceptor (+/-2bp)		2	3			5
splice region			4	8	1	13
non coding			2	37	27	66
Total	1	5	101	78	36

Variants in BICC1

This is a list of pathogenic ClinVar variants found in the BICC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-58512948-T-C			Benign (Nov 10, 2018)
10-58513048-C-T			Likely benign (Jan 13, 2020)
10-58513093-G-A			Benign (Nov 02, 2020)
10-58513164-C-T			Likely benign (Dec 20, 2023)
10-58513169-A-T			Uncertain significance (May 23, 2023)
10-58513171-C-T			Likely benign (Jul 12, 2023)
10-58513175-C-G			Uncertain significance (Sep 17, 2023)
10-58513184-C-T		Renal dysplasia, cystic, susceptibility to	Uncertain significance (May 31, 2022)
10-58513189-C-A			Uncertain significance (Jul 27, 2022)
10-58513234-TC-T		Renal dysplasia, cystic, susceptibility to	Pathogenic (Jan 07, 2021)
10-58513264-C-T			Likely benign (May 03, 2023)
10-58513272-C-G		Renal dysplasia, cystic, susceptibility to	Uncertain significance (Mar 07, 2022)
10-58513274-C-T			Likely benign (Oct 03, 2023)
10-58513281-G-T		not specified	Uncertain significance (Aug 22, 2023)
10-58513314-A-G			Likely benign (Jul 05, 2022)
10-58513324-A-G			Uncertain significance (Jun 27, 2023)
10-58513361-T-C			Benign (Nov 10, 2018)
10-58513395-C-A			Benign (Nov 10, 2018)
10-58513429-ACGGC-A			Benign (Nov 10, 2018)
10-58620793-C-T			Benign (Sep 06, 2019)
10-58620837-G-A			Likely benign (Jul 12, 2021)
10-58620871-A-G			Likely benign (Nov 27, 2023)
10-58620901-G-A			Uncertain significance (Nov 01, 2022)
10-58620909-G-A			Likely benign (Jan 02, 2024)
10-58620945-A-G			Likely benign (Apr 28, 2020)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BICC1	protein_coding	protein_coding	ENST00000373886	21	318296

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.837	0.163	125710	0	20	125730	0.0000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.25	449	530	0.848	0.0000270	6346
Missense in Polyphen		109	164.42	0.66292		2038
Synonymous	-0.440	205	197	1.04	0.0000105	1928
Loss of Function	5.24	10	50.0	0.200	0.00000283	584

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000203	0.000203
Ashkenazi Jewish	0.00	0.00
East Asian	0.000172	0.000163
Finnish	0.0000945	0.0000924
European (Non-Finnish)	0.0000445	0.0000440
Middle Eastern	0.000172	0.000163
South Asian	0.0000981	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Putative RNA-binding protein. Acts as a negative regulator of Wnt signaling. May be involved in regulating gene expression during embryonic development. {ECO:0000269|PubMed:21922595}.
• Disease: DISEASE: Renal dysplasia, cystic (CYSRD) [MIM:601331]: An anomaly of the kidney characterized by numerous renal cysts and apparent disorder of differentiation of the renal parenchyma. Kidney of affected individuals lack the normal renal bean shape, and the collection drainage system. The cystic, dysplastic kidney contains undifferentiated mesenchyme, cartilaginous tissue, and immature collecting ducts. {ECO:0000269|PubMed:21922595}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.

Recessive Scores

• pRec: 0.118

Intolerance Scores

• loftool: 0.459
• rvis_EVS: 0.6
• rvis_percentile_EVS: 82.87

Haploinsufficiency Scores

• pHI: 0.207
• hipred: N
• hipred_score: 0.416
• ghis: 0.508

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.153

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Bicc1
• Phenotype: endocrine/exocrine gland phenotype; growth/size/body region phenotype; homeostasis/metabolism phenotype; cellular phenotype; digestive/alimentary phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); liver/biliary system phenotype; embryo phenotype; renal/urinary system phenotype

Gene ontology

• Biological process: determination of left/right symmetry;heart development;negative regulation of canonical Wnt signaling pathway
• Cellular component: cytoplasm
• Molecular function: RNA binding