ARNT2-DT

ARNT2 divergent transcript, the group of Divergent transcripts

Basic information

Region (hg38): 15:80344765-80411930

Links

ENSG00000259495 ∙ NCBI:101929560 ∙ ∙ HGNC:56077 ∙ ∙ ∙ 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 ARNT2-DT gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARNT2-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						0
Total	0	0	0	0	0

Variants in ARNT2-DT

This is a list of pathogenic ClinVar variants found in the ARNT2-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
15-80404522-A-G			Uncertain significance (Jun 04, 2022)
15-80404523-C-A		not specified	Uncertain significance (Dec 01, 2022)
15-80404524-C-T			Likely benign (Jun 14, 2018)
15-80404533-G-C			Likely benign (Jul 17, 2022)
15-80404543-C-T			Uncertain significance (Sep 27, 2022)
15-80410644-A-G		Pulmonary disease, chronic obstructive, susceptibility to	association (May 13, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ARNT2-DT	protein_coding	protein_coding	ENST00000559008	3	58723

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0237	0.562	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.385	27	33.2	0.812	0.00000205	358
Missense in Polyphen
Synonymous	0.581	8	10.4	0.771	5.72e-7	106
Loss of Function	-0.0669	2	1.90	1.05	8.03e-8	25

LoF frequencies by population

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

dbNSFP

Source: dbNSFP