BICRA

BRD4 interacting chromatin remodeling complex associated protein, the group of GBAF complex

Basic information

Region (hg38): 19:47608195-47703277

Previous symbols: [ "GLTSCR1" ]

Links

ENSG00000063169 ∙ NCBI:29998 ∙ OMIM:605690 ∙ HGNC:4332 ∙ Uniprot:Q9NZM4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Coffin-Siris syndrome 12 (Moderate), mode of inheritance: AD

ClinVar

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

• Coffin-Siris syndrome 12 (7 variants)
• not provided (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BICRA 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			1	26	9	36
missense		1	186	9	5	201
nonsense	3	3	1			7
start loss						0
frameshift	8	4	6			18
inframe indel			2		1	3
splice donor/acceptor (+/-2bp)	1				1	2
splice region			1	3		4
non coding					3	3
Total	12	8	196	35	19

Variants in BICRA

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

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

Position	Type	Phenotype	Significance	ClinVar
19-47608282-G-A			Uncertain significance (Feb 05, 2021)
19-47673720-T-C		not specified	Likely benign (Jul 13, 2023)
19-47673756-C-T			Likely benign (May 01, 2022)
19-47675854-G-C			Uncertain significance (May 15, 2022)
19-47675857-A-G		not specified	Uncertain significance (May 23, 2023)
19-47675864-ACCT-A			Uncertain significance (Nov 06, 2021)
19-47675868-C-T			Likely benign (Jul 01, 2024)
19-47675881-G-A		not specified	Uncertain significance (Aug 26, 2022)
19-47675903-A-G		not specified	Uncertain significance (Jun 22, 2023)
19-47675911-C-T		Coffin-Siris syndrome 12	Uncertain significance (Feb 09, 2023)
19-47679311-C-T			Benign (Feb 24, 2022)
19-47679362-G-C		Coffin-Siris syndrome 12	Pathogenic (May 20, 2021)
19-47679421-C-G		not specified	Uncertain significance (Mar 14, 2023)
19-47679432-G-A		BICRA-related disorder	Uncertain significance (Jan 27, 2023)
19-47679441-G-A		BICRA-related disorder	Likely benign (Oct 21, 2022)
19-47679444-G-A		not specified	Uncertain significance (Feb 14, 2024)
19-47679460-C-T		not specified	Uncertain significance (Mar 02, 2023)
19-47679504-A-G		Coffin-Siris syndrome 12	Uncertain significance (Feb 17, 2023)
19-47679507-A-G			Uncertain significance (Mar 16, 2023)
19-47679508-T-G			Uncertain significance (Jun 03, 2021)
19-47679520-C-T			Uncertain significance (Oct 25, 2022)
19-47679530-C-T		BICRA-related disorder	Benign (Feb 01, 2023)
19-47679531-G-C			Uncertain significance (Nov 01, 2023)
19-47679551-TCCCTTCCAGCTGCCCA-T		Coffin-Siris syndrome 12	Likely pathogenic (Oct 20, 2021)
19-47679552-C-T		not specified	Uncertain significance (Jul 08, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BICRA	protein_coding	protein_coding	ENST00000396720	13	95081

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.983	0.0165	120322	0	2	120324	0.00000831

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.54	618	823	0.751	0.0000561	9533
Missense in Polyphen		123	201.36	0.61084		2114
Synonymous	-1.41	460	423	1.09	0.0000355	3509
Loss of Function	4.66	5	34.5	0.145	0.00000149	429

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000619	0.0000569
Finnish	0.00	0.00
European (Non-Finnish)	0.00000963	0.00000918
Middle Eastern	0.0000619	0.0000569
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of SWI/SNF chromatin remodeling subcomplex GBAF that carries out key enzymatic activities, changing chromatin structure by altering DNA-histone contacts within a nucleosome in an ATP-dependent manner (PubMed:29374058). May play a role in BRD4-mediated gene transcription (PubMed:21555454). {ECO:0000269|PubMed:21555454, ECO:0000269|PubMed:29374058}.

Recessive Scores

• pRec: 0.125

Haploinsufficiency Scores

• pHI: 0.160
• hipred: Y
• hipred_score: 0.523
• ghis: 0.446

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Bicra

Gene ontology

• Biological process: positive regulation of transcription, DNA-templated
• Cellular component: nucleus;SWI/SNF complex
• Molecular function: transcription coactivator activity;protein binding