ATXN1L

ataxin 1 like

Basic information

Region (hg38): 16:71808439-71885268

Links

ENSG00000224470 ∙ NCBI:342371 ∙ OMIM:614301 ∙ HGNC:33279 ∙ Uniprot:P0C7T5 ∙ 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 ATXN1L gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATXN1L 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			46	2		48
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	46	2	0

Variants in ATXN1L

This is a list of pathogenic ClinVar variants found in the ATXN1L region.

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

Position	Type	Phenotype	Significance	ClinVar
16-71849771-T-C		not specified	Uncertain significance (Apr 22, 2024)
16-71849801-G-A		not specified	Uncertain significance (Feb 05, 2024)
16-71849829-C-T		not specified	Uncertain significance (Jun 03, 2024)
16-71849900-C-A		not specified	Uncertain significance (Apr 23, 2024)
16-71849931-G-T		not specified	Uncertain significance (May 15, 2023)
16-71849999-G-A		not specified	Uncertain significance (Sep 01, 2021)
16-71850060-C-T		not specified	Uncertain significance (Sep 07, 2022)
16-71850065-A-G		not specified	Uncertain significance (Mar 11, 2022)
16-71850066-C-A		not specified	Uncertain significance (Sep 27, 2021)
16-71850098-C-T		not specified	Uncertain significance (Apr 20, 2024)
16-71850111-A-G		not specified	Uncertain significance (Mar 25, 2024)
16-71850116-C-A		not specified	Uncertain significance (Jan 18, 2022)
16-71850162-G-C		not specified	Uncertain significance (Dec 16, 2023)
16-71850243-C-T		not specified	Uncertain significance (Apr 13, 2023)
16-71850285-C-A		not specified	Uncertain significance (Jun 21, 2021)
16-71850330-C-T		not specified	Uncertain significance (Jan 31, 2023)
16-71850399-T-C		not specified	Uncertain significance (Dec 19, 2022)
16-71850425-A-G		not specified	Uncertain significance (Mar 17, 2023)
16-71850439-G-A		not specified	Uncertain significance (Apr 06, 2023)
16-71850479-C-A		not specified	Uncertain significance (Nov 18, 2022)
16-71850489-C-A		not specified	Uncertain significance (Sep 16, 2021)
16-71850504-C-T		not specified	Uncertain significance (May 02, 2024)
16-71850514-G-C		not specified	Uncertain significance (Jun 14, 2023)
16-71850516-G-T		not specified	Uncertain significance (Sep 01, 2021)
16-71850524-G-C		not specified	Uncertain significance (Apr 26, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ATXN1L	protein_coding	protein_coding	ENST00000427980	1	39278

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.979	0.0210	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.08	323	382	0.844	0.0000213	4390
Missense in Polyphen		80	112.28	0.71249		1338
Synonymous	1.43	136	159	0.856	0.00000915	1538
Loss of Function	3.80	2	20.6	0.0969	0.00000139	211

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Chromatin-binding factor that repress Notch signaling in the absence of Notch intracellular domain by acting as a CBF1 corepressor. Binds to the HEY promoter and might assist, along with NCOR2, RBPJ-mediated repression (PubMed:21475249). Can suppress ATXN1 cytotoxicity in spinocerebellar ataxia type 1 (SCA1). In concert with CIC and ATXN1, involved in brain development (By similarity). {ECO:0000250|UniProtKB:P0C7T6, ECO:0000269|PubMed:21475249}.

Intolerance Scores

• rvis_EVS: 0.64
• rvis_percentile_EVS: 83.78

Haploinsufficiency Scores

• ghis: 0.411

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.734

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Atxn1l
• Phenotype: respiratory system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); skeleton phenotype; growth/size/body region phenotype; craniofacial phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;brain development;learning;memory;extracellular matrix organization;social behavior;lung alveolus development;positive regulation of hematopoietic stem cell proliferation
• Cellular component: nucleus;nucleoplasm;nucleolus;dendrite
• Molecular function: DNA binding;RNA binding;protein binding