ATXN7L2

ataxin 7 like 2

Basic information

Region (hg38): 1:109483478-109492804

Links

ENSG00000162650 ∙ NCBI:127002 ∙ ∙ HGNC:28713 ∙ Uniprot:Q5T6C5 ∙ 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 ATXN7L2 gene.

• Inborn genetic diseases (20 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATXN7L2 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			20			20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	0	0

Variants in ATXN7L2

This is a list of pathogenic ClinVar variants found in the ATXN7L2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-109483978-G-A		not specified	Uncertain significance (May 26, 2023)
1-109484043-C-G		not specified	Uncertain significance (Mar 07, 2023)
1-109484053-G-A		not specified	Uncertain significance (Jul 09, 2021)
1-109486527-G-T		not specified	Uncertain significance (Jan 29, 2024)
1-109487033-C-G		not specified	Uncertain significance (Sep 29, 2022)
1-109487042-C-T		not specified	Uncertain significance (Oct 04, 2022)
1-109487169-G-A		not specified	Uncertain significance (Jan 16, 2024)
1-109487709-C-T		not specified	Uncertain significance (Aug 16, 2021)
1-109488398-T-G		not specified	Uncertain significance (Oct 03, 2022)
1-109488859-C-A		not specified	Uncertain significance (Dec 22, 2023)
1-109488901-G-A		not specified	Uncertain significance (Jun 09, 2022)
1-109488931-C-T		not specified	Uncertain significance (Aug 23, 2021)
1-109488985-G-A		not specified	Uncertain significance (Feb 21, 2024)
1-109488988-C-T		not specified	Uncertain significance (Jan 02, 2024)
1-109489031-C-T		not specified	Uncertain significance (Jul 12, 2023)
1-109489940-T-G		not specified	Uncertain significance (Feb 28, 2024)
1-109490018-C-T		not specified	Uncertain significance (Mar 20, 2023)
1-109490061-G-A		not specified	Uncertain significance (Dec 22, 2023)
1-109490081-C-G		not specified	Uncertain significance (Nov 23, 2021)
1-109490097-A-G		not specified	Uncertain significance (Nov 15, 2021)
1-109490326-G-A		not specified	Uncertain significance (Dec 05, 2022)
1-109490969-C-G		not specified	Uncertain significance (Dec 02, 2022)
1-109490969-C-T		not specified	Uncertain significance (Jan 16, 2024)
1-109490971-T-A		not specified	Uncertain significance (Jan 06, 2023)
1-109491004-A-T		not specified	Likely benign (Dec 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ATXN7L2	protein_coding	protein_coding	ENST00000369870	11	9326

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.871	0.129	125739	0	7	125746	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.16	363	431	0.843	0.0000255	4629
Missense in Polyphen		97	152.55	0.63586		1570
Synonymous	-0.320	171	166	1.03	0.00000901	1526
Loss of Function	3.81	4	24.3	0.165	0.00000111	326

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000132	0.000120
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000580	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000185	0.0000176
Middle Eastern	0.0000580	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0743

Intolerance Scores

• loftool: 0.226
• rvis_EVS: -0.91
• rvis_percentile_EVS: 10.03

Haploinsufficiency Scores

• pHI: 0.263
• hipred: N
• hipred_score: 0.485
• ghis: 0.532

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.695

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Atxn7l2