BCLAF1

BCL2 associated transcription factor 1, the group of WTAP complex

Basic information

Region (hg38): 6:136256627-136289851

Links

ENSG00000029363 ∙ NCBI:9774 ∙ OMIM:612588 ∙ HGNC:16863 ∙ Uniprot:Q9NYF8 ∙ 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 BCLAF1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BCLAF1 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				12		12
missense			41	4	4	49
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region				1		1
non coding						0
Total	0	0	42	16	4

Variants in BCLAF1

This is a list of pathogenic ClinVar variants found in the BCLAF1 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-136261279-G-A		not specified	Benign (Mar 29, 2016)
6-136261359-G-T		not specified • BCLAF1-related disorder	Benign (Mar 29, 2016)
6-136261374-C-T		BCLAF1-related disorder	Likely benign (Apr 05, 2023)
6-136267084-G-A		not specified	Uncertain significance (Mar 29, 2024)
6-136268161-C-G		not specified	Uncertain significance (Mar 29, 2016)
6-136268269-G-T		BCLAF1-related disorder	Likely benign (May 19, 2023)
6-136268271-G-A		not specified	Uncertain significance (Nov 17, 2022)
6-136268277-G-A		not specified	Uncertain significance (Nov 05, 2021)
6-136268287-G-A		not specified	Uncertain significance (Sep 14, 2021)
6-136268287-G-T		not specified • BCLAF1-related disorder	Benign (Mar 29, 2016)
6-136269475-T-C		not specified	Likely benign (Dec 10, 2021)
6-136269502-A-C		BCLAF1-related disorder	Benign (Apr 16, 2020)
6-136269560-C-T		not specified • BCLAF1-related disorder	Benign (Mar 29, 2016)
6-136269574-C-T		not specified	Likely benign (Dec 03, 2021)
6-136269614-T-TTTTG		BCLAF1-related disorder	Likely benign (Feb 23, 2021)
6-136271998-T-G		not specified	Uncertain significance (Jan 04, 2024)
6-136272017-A-G		not specified	Uncertain significance (Dec 09, 2023)
6-136273086-G-T		not specified	Uncertain significance (Jul 05, 2023)
6-136273100-T-C		not specified	Uncertain significance (Jun 23, 2021)
6-136273117-T-C			Likely benign (Jul 20, 2018)
6-136273153-G-A			Likely benign (Jun 29, 2018)
6-136273164-T-C		not specified	Likely benign (Sep 01, 2021)
6-136275550-A-C		not specified	Uncertain significance (Dec 10, 2021)
6-136275552-G-A		not specified	Uncertain significance (Jun 24, 2022)
6-136275663-G-A		not specified	Uncertain significance (May 28, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BCLAF1	protein_coding	protein_coding	ENST00000531224	11	32989

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.06e-14	0.810	123059	0	2687	125746	0.0107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-4.36	667	417	1.60	0.0000219	5477
Missense in Polyphen		36	22.244	1.6184		256
Synonymous	-7.26	252	142	1.77	0.00000725	1582
Loss of Function	1.92	28	41.3	0.678	0.00000279	531

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00623	0.00623
Ashkenazi Jewish	0.0125	0.0125
East Asian	0.00606	0.00605
Finnish	0.0160	0.0159
European (Non-Finnish)	0.00784	0.00777
Middle Eastern	0.00606	0.00605
South Asian	0.0329	0.0328
Other	0.0116	0.0116

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Death-promoting transcriptional repressor. May be involved in cyclin-D1/CCND1 mRNA stability through the SNARP complex which associates with both the 3'end of the CCND1 gene and its mRNA. {ECO:0000269|PubMed:18794151}.
• Pathway: Interactome of polycomb repressive complex 2 (PRC2) (Consensus)

Recessive Scores

• pRec: 0.182

Intolerance Scores

• loftool: 0.873
• rvis_EVS: 1.99
• rvis_percentile_EVS: 97.64

Haploinsufficiency Scores

• pHI: 0.858
• ghis: 0.558

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 1.00

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Bclaf1
• Phenotype: homeostasis/metabolism phenotype; cellular phenotype; growth/size/body region phenotype; limbs/digits/tail phenotype; immune system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system phenotype; hematopoietic system phenotype; 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)

Gene ontology

• Biological process: apoptotic process;positive regulation of apoptotic process;regulation of DNA-templated transcription in response to stress;negative regulation of transcription, DNA-templated;cellular response to leukemia inhibitory factor;positive regulation of DNA-templated transcription, initiation;positive regulation of response to DNA damage stimulus;positive regulation of intrinsic apoptotic signaling pathway
• Cellular component: nucleus;nucleoplasm;cytoplasm;nuclear speck
• Molecular function: DNA binding;RNA binding;protein binding