ATF6B

activating transcription factor 6 beta, the group of Basic leucine zipper proteins

Basic information

Region (hg38): 6:32115264-32128253

Previous symbols: [ "CREBL1" ]

Links

ENSG00000213676 ∙ NCBI:1388 ∙ OMIM:600984 ∙ HGNC:2349 ∙ Uniprot:Q99941 ∙ 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 ATF6B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATF6B 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		1
missense			30	6		36
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	30	7	0

Variants in ATF6B

This is a list of pathogenic ClinVar variants found in the ATF6B region.

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

Position	Type	Phenotype	Significance	ClinVar
6-32115764-T-A		not specified	Uncertain significance (Jan 26, 2022)
6-32115791-G-T		not specified	Uncertain significance (Nov 18, 2022)
6-32115953-C-T		not specified	Uncertain significance (Jun 02, 2023)
6-32116560-T-A			Likely benign (May 21, 2018)
6-32116738-C-T		not specified	Uncertain significance (Sep 28, 2022)
6-32116741-C-T		not specified	Uncertain significance (Dec 06, 2021)
6-32116787-G-A		not specified	Uncertain significance (Nov 08, 2022)
6-32117095-G-A		not specified	Likely benign (Apr 05, 2023)
6-32117315-C-T			Benign (Jul 10, 2018)
6-32117378-A-G		not specified	Uncertain significance (Jan 11, 2023)
6-32117394-C-T		not specified	Uncertain significance (Apr 27, 2023)
6-32117886-G-A		not specified	Likely benign (Jan 04, 2022)
6-32117916-C-T		not specified	Likely benign (Oct 03, 2023)
6-32117920-G-T		not specified	Uncertain significance (Jan 18, 2022)
6-32117932-C-T		not specified	Uncertain significance (Jun 11, 2021)
6-32117965-G-C		not specified	Uncertain significance (Feb 10, 2023)
6-32118018-G-A		not specified	Uncertain significance (Oct 04, 2022)
6-32118034-T-C		not specified	Uncertain significance (Jul 05, 2023)
6-32118978-C-T		not specified	Likely benign (May 24, 2024)
6-32119101-C-T		not specified	Uncertain significance (May 30, 2023)
6-32119832-C-G		not specified	Uncertain significance (Feb 15, 2023)
6-32119871-T-G		not specified	Uncertain significance (Apr 18, 2023)
6-32119911-T-G		not specified	Uncertain significance (Apr 05, 2023)
6-32120879-G-A		not specified	Uncertain significance (May 13, 2022)
6-32120885-G-A		not specified	Uncertain significance (Apr 09, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ATF6B	protein_coding	protein_coding	ENST00000375203	18	30078

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.10e-7	0.999	125711	0	36	125747	0.000143

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.53	315	401	0.785	0.0000217	4489
Missense in Polyphen		120	157.78	0.76056		1779
Synonymous	1.32	144	166	0.870	0.00000870	1522
Loss of Function	2.98	17	36.4	0.466	0.00000188	397

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000145	0.000145
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.000326	0.000326
Finnish	0.00	0.00
European (Non-Finnish)	0.000172	0.000158
Middle Eastern	0.000326	0.000326
South Asian	0.000164	0.000163
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcriptional factor that acts in the unfolded protein response (UPR) pathway by activating UPR target genes induced during ER stress. Binds DNA on the 5'-CCAC[GA]-3' half of the ER stress response element (ERSE) (5'-CCAATN(9)CCAC[GA]-3') when NF-Y is bound to ERSE.
• Pathway: PI3K-Akt signaling pathway - Homo sapiens (human);Cortisol synthesis and secretion - Homo sapiens (human);Relaxin signaling pathway - Homo sapiens (human);Aldosterone synthesis and secretion - Homo sapiens (human);Dopaminergic synapse - Homo sapiens (human);Cushing,s syndrome - Homo sapiens (human);Thyroid hormone synthesis - Homo sapiens (human);Protein processing in endoplasmic reticulum - Homo sapiens (human);TNF signaling pathway - Homo sapiens (human);Adrenergic signaling in cardiomyocytes - Homo sapiens (human);Longevity regulating pathway - Homo sapiens (human);Estrogen signaling pathway - Homo sapiens (human);Amphetamine addiction - Homo sapiens (human);Viral carcinogenesis - Homo sapiens (human);Hepatitis B - Homo sapiens (human);cGMP-PKG signaling pathway - Homo sapiens (human);Alcoholism - Homo sapiens (human);Cocaine addiction - Homo sapiens (human);Insulin secretion - Homo sapiens (human);Myometrial Relaxation and Contraction Pathways;Focal Adhesion-PI3K-Akt-mTOR-signaling pathway;PI3K-Akt Signaling Pathway;G1 to S cell cycle control (Consensus)

Intolerance Scores

• loftool: 0.858
• rvis_EVS: 0.13
• rvis_percentile_EVS: 63.57

Haploinsufficiency Scores

• pHI: 0.218
• hipred: Y
• hipred_score: 0.520
• ghis: 0.504

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.824

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Atf6b
• Phenotype: cellular phenotype; hearing/vestibular/ear 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: transcription, DNA-templated;signal transduction;ATF6-mediated unfolded protein response;positive regulation of transcription by RNA polymerase II;negative regulation of ATF6-mediated unfolded protein response;positive regulation of transcription from RNA polymerase II promoter in response to endoplasmic reticulum stress
• Cellular component: nucleus;nucleolus;endoplasmic reticulum membrane;Golgi apparatus;integral component of endoplasmic reticulum membrane;protein-DNA complex;RNA polymerase II transcription factor complex
• Molecular function: RNA polymerase II distal enhancer sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific;DNA-binding transcription factor activity;protein binding;cAMP response element binding;transcription regulatory region DNA binding