ATXN2L

protein-coding

ataxin 2 like

Gene summary

This gene encodes an ataxin type 2 related protein of unknown function. This protein is a member of the spinocerebellar ataxia (SCAs) family, which is associated with a complex group of neurodegenerative disorders. Several alternatively spliced transcripts encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

MANE transcript

NM_007245.4

Inheritance

ClinVar variants

U:156B:6

Top phenotype

Marfanoid habitus and intellectual disability

gnomAD constraint

pLI —, LoF o/e 0.06

Max pathogenic AF

—

Genomic locus

chr16:28,822,999-28,837,237

External References & Databases

Ensembl (ENSG00000168488)

Transcript & Mutation Effects

hg38 • Region Span ~14.2 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

neurodevelopmental disorderMODERATE

Inheritance Pattern: AD

Disease ID:MONDO:0700092

Submitter: PanelApp Australia

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ATXN2L variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 138

not providedTotal: 5

Marfanoid habitus and intellectual disabilityTotal: 1

Neurodevelopmental disorderTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_007245.4. 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			3 clinvar	3 clinvar	1 clinvar	7
missense			142 clinvar	2 clinvar		144
nonsense			1 clinvar			1
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			9 clinvar			9
Total	0	0	156	5	1	162

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 105 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_007245.4	RefSeq	NP_009176.2	22	MANE Select
ENST00000336783.9	Ensembl	ENSP00000338718.4	22	MANE Select
NM_001308230.2	RefSeq	NP_001295159.1	23	Standard
NM_001387166.1	RefSeq	NP_001374095.1	23	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

regulation of cytoplasmic mRNA processing body assembly
stress granule assembly

Molecular Function

RNA binding
protein binding
cadherin binding

Cellular Component

cytosol
cytoplasmic stress granule
membrane
nuclear speck

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000395547
Coding exons: 23
Length: 14203
Individuals with no LoFs: 125708
Homozygous LoFs: 0
Heterozygous LoFs: 40
Defined: 125748
p: 0.000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.25	471	630	0.748	0.0000372	6974
Missense (PolyPhen)		138	224.79	0.61391		2570
Synonymous	-2.80	309	252	1.22	0.0000158	2351
Loss of Function	6.46	3	54.4	0.0552	0.00000302	594

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.00076	0.00075	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000055	0.000054	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.000092	0.000088	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Involved in the regulation of stress granule and P-body formation. {ECO:0000269|PubMed:23209657}.;

Recessive Scores

pRec: 0.121

Intolerance Scores

RVIS EVS: -1.73
RVIS percentile EVS: 2.45

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.991

Gene Damage Prediction

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