ATXN7L1

ataxin 7 like 1

Basic information

Region (hg38): 7:105604772-105876599

Previous symbols: [ "ATXN7L4" ]

Links

ENSG00000146776 ∙ NCBI:222255 ∙ ∙ HGNC:22210 ∙ Uniprot:Q9ULK2 ∙ 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 ATXN7L1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATXN7L1 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			48	1		49
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	48	1	0

Variants in ATXN7L1

This is a list of pathogenic ClinVar variants found in the ATXN7L1 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-105610533-C-T		not specified	Uncertain significance (Sep 01, 2021)
7-105610584-A-G		not specified	Uncertain significance (Mar 14, 2023)
7-105613910-G-T		not specified	Uncertain significance (Mar 31, 2023)
7-105613918-G-A		not specified	Uncertain significance (Jun 23, 2023)
7-105613942-T-C		not specified	Uncertain significance (Jun 07, 2023)
7-105613986-G-C		not specified	Uncertain significance (May 24, 2024)
7-105614066-G-T		not specified	Uncertain significance (Nov 27, 2023)
7-105614077-G-A		not specified	Uncertain significance (Aug 17, 2022)
7-105614130-G-A		not specified	Uncertain significance (Mar 07, 2023)
7-105614155-C-T		not specified	Uncertain significance (May 31, 2022)
7-105614172-G-A		not specified	Uncertain significance (Feb 05, 2024)
7-105614230-T-G		not specified	Uncertain significance (Oct 02, 2023)
7-105614425-C-T		not specified	Uncertain significance (Nov 06, 2023)
7-105614441-G-T		not specified	Uncertain significance (Sep 16, 2021)
7-105614517-G-A		not specified	Uncertain significance (Apr 12, 2022)
7-105614593-T-C		not specified	Uncertain significance (Mar 20, 2023)
7-105614622-G-A		not specified	Uncertain significance (Apr 23, 2024)
7-105614665-T-A		not specified	Uncertain significance (Nov 08, 2022)
7-105614667-T-C		not specified	Uncertain significance (Oct 12, 2022)
7-105614755-C-T		not specified	Uncertain significance (Jul 21, 2021)
7-105614758-G-C		not specified	Uncertain significance (Feb 15, 2023)
7-105614770-G-A		not specified	Uncertain significance (Sep 20, 2023)
7-105620231-C-T		not specified	Uncertain significance (Mar 01, 2024)
7-105620257-C-T		not specified	Uncertain significance (Mar 19, 2024)
7-105620290-C-T		not specified	Uncertain significance (Jan 04, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ATXN7L1	protein_coding	protein_coding	ENST00000419735	12	271537

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.00116	125611	0	12	125623	0.0000478

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.30	336	477	0.704	0.0000266	5546
Missense in Polyphen		93	165.04	0.56351		2017
Synonymous	1.44	176	202	0.871	0.0000129	1816
Loss of Function	4.59	2	28.4	0.0703	0.00000140	393

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)	0.0000265	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.000296	0.000294
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0934

Intolerance Scores

• loftool: 0.510
• rvis_EVS: 0.17
• rvis_percentile_EVS: 65.96

Haploinsufficiency Scores

• pHI: 0.938
• hipred: N
• hipred_score: 0.306
• ghis: 0.433

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0319

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Atxn7l1

Gene ontology

• Molecular function: protein binding