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.

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.

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	2
missense			47			47
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	1	2
non coding					1	1
Total	0	0	47	1	2

Variants in ATXN2L

This is a list of pathogenic ClinVar variants found in the ATXN2L region.

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

Position	Type	Phenotype	Significance	ClinVar
16-28823281-C-A		not specified	Uncertain significance (Oct 13, 2023)
16-28823311-C-A		not specified	Uncertain significance (Mar 20, 2023)
16-28823347-G-T		not specified	Uncertain significance (Feb 23, 2023)
16-28823369-G-A		not specified	Uncertain significance (Feb 22, 2023)
16-28823390-C-A		not specified	Uncertain significance (Feb 15, 2023)
16-28823434-C-G		not specified	Uncertain significance (Apr 15, 2024)
16-28823458-A-G		not specified	Uncertain significance (Jan 08, 2024)
16-28823483-G-A		not specified	Uncertain significance (Feb 10, 2022)
16-28825649-C-G		not specified	Uncertain significance (Apr 08, 2022)
16-28825688-G-A			Benign (Apr 04, 2018)
16-28826258-G-A		not specified	Uncertain significance (Dec 09, 2023)
16-28826267-C-T		not specified	Uncertain significance (Dec 09, 2023)
16-28826297-C-T		not specified	Uncertain significance (Dec 14, 2023)
16-28826865-A-G		not specified	Uncertain significance (Jun 02, 2023)
16-28826890-G-A		not specified	Uncertain significance (Mar 04, 2024)
16-28826933-C-T		not specified	Uncertain significance (May 16, 2023)
16-28826934-G-T		not specified	Uncertain significance (Oct 21, 2021)
16-28829901-G-C		not specified	Uncertain significance (Feb 03, 2022)
16-28829953-G-A		not specified	Uncertain significance (Jul 06, 2021)
16-28829961-A-G		not specified	Uncertain significance (Dec 06, 2022)
16-28829968-T-C		Marfanoid habitus and intellectual disability	Uncertain significance (-)
16-28830010-C-T		not specified	Uncertain significance (Nov 10, 2022)
16-28830034-G-A		not specified	Uncertain significance (May 04, 2023)
16-28830644-G-A		not specified	Uncertain significance (Nov 21, 2023)
16-28830694-G-A		not specified	Uncertain significance (Dec 12, 2023)

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

• 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

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