ATXN3L

protein-coding

ataxin 3 like, the group of MJD deubiquinating enzymes

Gene summary

This intronless gene may be a pseudogene (PMID:11450850). This gene is similar to the multi-exon gene which encodes ataxin 3 and contains a coding region which could encode a protein similar to ataxin 3. Mutations in the gene encoding ataxin 3 are associated with Machado-Joseph disease. [provided by RefSeq, Sep 2011]

MANE transcript

NM_001135995.2

Inheritance

—

ClinVar variants

U:34B:6

Top phenotype

Intellectual disability

gnomAD constraint

pLI —, LoF o/e —

Max pathogenic AF

—

Genomic locus

chrX:13,318,647-13,320,053

External References & Databases

Ensembl (ENSG00000123594)

Transcript & Mutation Effects

hg38 • Region Span ~1.4 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ATXN3L variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 39

not providedTotal: 3

Intellectual disabilityTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001135995.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			34 clinvar	5 clinvar		39
nonsense				1 clinvar		1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	34	6	0	40

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 3 of 3 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001135995.2	RefSeq	NP_001129467.1	1	MANE Select
ENST00000380622.5	Ensembl	ENSP00000369996.2	1	MANE Select
NM_001387036.1	RefSeq	NP_001373965.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Protein processing in endoplasmic reticulum - Homo sapiens (human)
Josephin domain DUBs
Post-translational protein modification
Metabolism of proteins
Deubiquitination

Biological Process

protein deubiquitination

Molecular Function

thiol-dependent ubiquitin-specific protease activity
thiol-dependent ubiquitinyl hydrolase activity

Cellular Component

nucleus
cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000380622
Coding exons: 1
Length: 1749

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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Deubiquitinating enzyme that cleaves both 'Lys-48'- linked and 'Lys-63'-linked poly-ubiquitin chains (in vitro).;

Recessive Scores

pRec: 0.104

Intolerance Scores

LoFtool: 0.801
RVIS EVS: 0.82
RVIS percentile EVS: 87.87

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0860

Gene Damage Prediction

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