B4GAT1-DT

B4GAT1 divergent transcript, the group of Divergent transcripts

Basic information

Region (hg38): 11:66347845-66364804

Links

ENSG00000255468 ∙ NCBI:102724064 ∙ ∙ HGNC:56070 ∙ ∙ ∙ 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 B4GAT1-DT gene.

• Inborn genetic diseases (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the B4GAT1-DT 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						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			2			2
Total	0	0	2	0	0

Variants in B4GAT1-DT

This is a list of pathogenic ClinVar variants found in the B4GAT1-DT region.

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

Position	Type	Phenotype	Significance	ClinVar
11-66363470-G-T		not specified	Uncertain significance (Dec 16, 2023)
11-66363516-C-T		not specified	Uncertain significance (Jan 03, 2024)
11-66364286-T-C		not specified	Uncertain significance (Aug 22, 2023)
11-66364346-C-T		not specified	Uncertain significance (Nov 02, 2023)
11-66364408-C-T		not specified	Uncertain significance (Feb 23, 2023)
11-66364409-G-A		not specified	Uncertain significance (Jun 12, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
B4GAT1-DT	protein_coding	protein_coding	ENST00000531602	1	16855

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0214	0.542	111023	4	1577	112604	0.00705

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.831	42	60.1	0.698	0.00000347	649
Missense in Polyphen
Synonymous	0.801	24	29.5	0.813	0.00000221	219
Loss of Function	-0.187	2	1.73	1.15	7.28e-8	24

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00558	0.00557
Ashkenazi Jewish	0.0137	0.0137
East Asian	0.0000609	0.0000606
Finnish	0.00334	0.00333
European (Non-Finnish)	0.0103	0.0102
Middle Eastern	0.0000609	0.0000606
South Asian	0.00595	0.00595
Other	0.00805	0.00805

dbNSFP

Source: dbNSFP