ATXN3L

ataxin 3 like, the group of MJD deubiquinating enzymes

Basic information

Region (hg38): X:13318647-13320053

Links

ENSG00000123594 ∙ NCBI:92552 ∙ OMIM:300920 ∙ HGNC:24173 ∙ Uniprot:Q9H3M9 ∙ 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 ATXN3L gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATXN3L 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			12	1		13
nonsense						0
start loss						0
frameshift						0
inframe indel				1		1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	2	0

Variants in ATXN3L

This is a list of pathogenic ClinVar variants found in the ATXN3L region.

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

Position	Type	Phenotype	Significance	ClinVar
X-13318985-CTTG-C			Likely benign (Mar 01, 2023)
X-13318988-G-A		not specified	Conflicting classifications of pathogenicity (Dec 18, 2023)
X-13319002-G-T		not specified	Uncertain significance (May 14, 2024)
X-13319070-T-A		Intellectual disability	Likely benign (Dec 01, 2017)
X-13319100-G-A		not specified	Uncertain significance (Oct 06, 2022)
X-13319157-C-T		not specified	Likely benign (May 27, 2022)
X-13319172-T-C		not specified	Conflicting classifications of pathogenicity (Feb 28, 2024)
X-13319240-G-A		not specified	Uncertain significance (Aug 02, 2022)
X-13319370-G-A		not specified	Uncertain significance (Oct 05, 2022)
X-13319385-C-T		not specified	Uncertain significance (Jun 16, 2024)
X-13319407-T-A		not specified	Uncertain significance (Apr 07, 2022)
X-13319429-A-G		not specified	Uncertain significance (Apr 29, 2024)
X-13319477-G-A		not specified	Uncertain significance (May 29, 2024)
X-13319531-G-A		not specified	Uncertain significance (Jan 24, 2024)
X-13319571-T-C		not specified	Uncertain significance (Oct 10, 2023)
X-13319574-A-G		not specified	Uncertain significance (Apr 22, 2024)
X-13319628-C-T		not specified	Uncertain significance (Jan 11, 2023)
X-13319637-G-C		not specified	Uncertain significance (Jan 03, 2022)
X-13319718-C-A		not specified	Uncertain significance (Apr 24, 2024)
X-13319735-T-C		not specified	Uncertain significance (Mar 29, 2022)
X-13319741-G-T		not specified	Uncertain significance (Mar 01, 2023)
X-13319786-T-C		not specified	Uncertain significance (Mar 26, 2024)
X-13319822-T-G		not specified	Uncertain significance (Dec 21, 2022)
X-13319859-C-T		not specified	Uncertain significance (Mar 28, 2024)
X-13319888-T-C		not specified	Uncertain significance (Aug 02, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ATXN3L	protein_coding	protein_coding	ENST00000380622	1	1749

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0203	128	127	1.01	0.00000914	2371
Missense in Polyphen		24	27.738	0.86523		559
Synonymous	0.155	49	50.4	0.972	0.00000402	626
Loss of Function

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Deubiquitinating enzyme that cleaves both 'Lys-48'- linked and 'Lys-63'-linked poly-ubiquitin chains (in vitro).
• Pathway: Protein processing in endoplasmic reticulum - Homo sapiens (human);Josephin domain DUBs;Post-translational protein modification;Metabolism of proteins;Deubiquitination (Consensus)

Recessive Scores

• pRec: 0.104

Intolerance Scores

• loftool: 0.801
• rvis_EVS: 0.82
• rvis_percentile_EVS: 87.87

Haploinsufficiency Scores

• pHI: 0.209
• hipred: N
• hipred_score: 0.267

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0860

Gene Damage Prediction

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

Gene ontology

• Biological process: protein deubiquitination
• Cellular component: nucleus;cytosol
• Molecular function: thiol-dependent ubiquitin-specific protease activity;thiol-dependent ubiquitinyl hydrolase activity