ATXN7L3

ataxin 7 like 3, the group of SAGA complex

Basic information

Region (hg38): 17:44191805-44200113

Links

ENSG00000087152 ∙ NCBI:56970 ∙ OMIM:619010 ∙ HGNC:25416 ∙ Uniprot:Q14CW9 ∙ 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 ATXN7L3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATXN7L3 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			14	1		15
nonsense			1			1
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	16	1	1

Variants in ATXN7L3

This is a list of pathogenic ClinVar variants found in the ATXN7L3 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-44194291-G-A		not specified	Uncertain significance (Aug 21, 2023)
17-44194326-G-C		not specified	Uncertain significance (Feb 07, 2023)
17-44194340-C-T		not specified	Likely benign (Sep 14, 2023)
17-44194360-C-T		not specified	Uncertain significance (Mar 31, 2023)
17-44194600-C-T		not specified	Uncertain significance (Oct 26, 2022)
17-44194677-G-A			Benign (Aug 08, 2017)
17-44194778-C-T		not specified	Uncertain significance (Jan 03, 2024)
17-44195422-G-A			Benign (Apr 19, 2018)
17-44195447-G-A		not specified	Uncertain significance (Apr 07, 2022)
17-44195475-T-C		not specified	Uncertain significance (Nov 18, 2022)
17-44196418-G-A		not specified	Uncertain significance (Aug 30, 2022)
17-44197018-T-C		not specified	Uncertain significance (Mar 31, 2024)
17-44197234-T-C		not specified	Uncertain significance (Nov 18, 2022)
17-44197244-G-A		See cases	Uncertain significance (-)
17-44197249-C-CT		See cases	Uncertain significance (-)
17-44197267-A-G		See cases	Uncertain significance (-)
17-44197308-G-C		See cases	Uncertain significance (-)
17-44197372-A-G		See cases	Uncertain significance (-)
17-44197725-G-C		not specified	Uncertain significance (Jun 10, 2024)
17-44197729-G-C		not specified	Uncertain significance (Jun 07, 2023)
17-44198026-T-A		not specified	Uncertain significance (Oct 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ATXN7L3	protein_coding	protein_coding	ENST00000454077	12	8309

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.00108	124784	0	2	124786	0.00000801

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.05	134	220	0.610	0.0000135	2356
Missense in Polyphen		9	56.395	0.15959		639
Synonymous	-0.673	93	85.1	1.09	0.00000558	627
Loss of Function	4.37	1	24.2	0.0413	0.00000137	257

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)	0.0000177	0.0000177
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the transcription regulatory histone acetylation (HAT) complex SAGA, a multiprotein complex that activates transcription by remodeling chromatin and mediating histone acetylation and deubiquitination. Within the SAGA complex, participates in a subcomplex that specifically deubiquitinates both histones H2A and H2B (PubMed:18206972, PubMed:21746879). The SAGA complex is recruited to specific gene promoters by activators such as MYC, where it is required for transcription. Required for nuclear receptor-mediated transactivation. Within the complex, it is required to recruit USP22 and ENY2 into the SAGA complex (PubMed:18206972). Regulates H2B monoubiquitination (H2Bub1) levels. Affects subcellular distribution of ENY2, USP22 and ATXN7L3B (PubMed:27601583). {ECO:0000255|HAMAP-Rule:MF_03047, ECO:0000269|PubMed:18206972, ECO:0000269|PubMed:21746879, ECO:0000269|PubMed:27601583}.
• Pathway: Chromatin modifying enzymes;HATs acetylate histones;Chromatin organization (Consensus)

Recessive Scores

• pRec: 0.113

Intolerance Scores

• loftool: 0.134
• rvis_EVS: -0.63
• rvis_percentile_EVS: 17.03

Haploinsufficiency Scores

• pHI: 0.695
• hipred: Y
• hipred_score: 0.706
• ghis: 0.604

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.832

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Atxn7l3
• Phenotype: cellular 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); skeleton phenotype; limbs/digits/tail phenotype

Gene ontology

• Biological process: histone monoubiquitination;histone deubiquitination;positive regulation of transcription, DNA-templated
• Cellular component: SAGA complex;nucleus;DUBm complex
• Molecular function: transcription coactivator activity;protein binding;zinc ion binding;nuclear receptor transcription coactivator activity