ATXN2L

ataxin 2 like

Basic information

Region (hg38): 16:28822999-28837237

Links

ENSG00000168488

∙ NCBI:11273 ∙ OMIM:607931 ∙ HGNC:31326 ∙ Uniprot:Q8WWM7 ∙ 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 ATXN2L gene.

not_specified (119 variants)
not_provided (3 variants)
Marfanoid_habitus_and_intellectual_disability (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATXN2L gene is commonly pathogenic or not. These statistics are base on transcript: NM_000007245.4. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				2 clinvar	1 clinvar	3
missense			117 clinvar	2 clinvar		119
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	117	4	1

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ATXN2L	protein_coding	protein_coding	ENST00000395547	23	14203

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	3.73e-7	125708	0	40	125748	0.000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.25	471	630	0.748	0.0000372	6974
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000817	0.000817
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000545	0.0000544
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.0000921	0.0000879
Middle Eastern	0.0000545	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

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

loftool
rvis_EVS: -1.73
rvis_percentile_EVS: 2.45

Haploinsufficiency Scores

pHI: 0.451
hipred: Y
hipred_score: 0.675
ghis: 0.681

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: S
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.991

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Atxn2l
Phenotype

Gene ontology

Biological process: regulation of cytoplasmic mRNA processing body assembly;stress granule assembly
Cellular component: cytosol;cytoplasmic stress granule;membrane;nuclear speck
Molecular function: RNA binding;protein binding;cadherin binding