ATXN10

ataxin 10, the group of Armadillo like helical domain containing|MicroRNA protein coding host genes

Basic information

Region (hg38): 22:45671797-45845307

Previous symbols: [ "SCA10" ]

Links

ENSG00000130638

∙ NCBI:25814 ∙ OMIM:611150 ∙ HGNC:10549 ∙ Uniprot:Q9UBB4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed

Phenotypes

GenCC

Source: genCC

spinocerebellar ataxia type 10 (Supportive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Spinocerebellar ataxia 10	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Neurologic	11017075; 11506407; 15127363; 16717236; 17420323; 20301354; 20818609; 21236683; 21531163

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ATXN10 gene.

not provided (24 variants)
Inborn genetic diseases (9 variants)
Spinocerebellar ataxia type 10 (7 variants)
not specified (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATXN10 gene is commonly pathogenic or not.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				4		4
missense			11			11
nonsense			1			1
start loss						0
frameshift			1			1
inframe indel						0
splice variant			2			2
non coding	1			1	16	18
Total	1	0	15	5	16

Variants in ATXN10

This is a list of pathogenic ClinVar variants found in the ATXN10 region.

Position	Phenotype	Significance	ClinVar
22-45671813-C-T		Benign (Jun 20, 2021)	link
22-45672074-C-G	Inborn genetic diseases	Uncertain significance (Jan 03, 2022)	link
22-45672076-A-G	Spinocerebellar ataxia type 10	Uncertain significance (Oct 26, 2018)	link
22-45672094-C-A	Inborn genetic diseases	Uncertain significance (Aug 09, 2021)	link
22-45672139-C-T		Likely benign (-)	link
22-45672142-C-T	Inborn genetic diseases	Uncertain significance (Sep 27, 2021)	link
22-45672183-A-T	Spinocerebellar ataxia type 10	Uncertain significance (Mar 01, 2019)	link
22-45672264-G-A		Benign (Nov 10, 2018)	link
22-45689733-C-G	Inborn genetic diseases	Uncertain significance (Nov 12, 2021)	link
22-45693008-G-A	not specified • Spinocerebellar ataxia type 10	Likely benign (Apr 25, 2022)	link
22-45693025-A-G	Inborn genetic diseases	Uncertain significance (Oct 11, 2021)	link
22-45700063-T-C		Benign (Jun 19, 2021)	link
22-45700117-A-G		Benign (Jun 18, 2021)	link
22-45700294-G-T	Spinocerebellar ataxia type 10	Uncertain significance (Jul 22, 2021)	link
22-45702735-A-G	Inborn genetic diseases	Uncertain significance (Apr 01, 2022)	link
22-45702848-G-GT	Inborn genetic diseases	Uncertain significance (Sep 02, 2021)	link
22-45718267-C-T		Benign (Nov 10, 2018)	link
22-45718364-C-T		Benign (Jun 18, 2021)	link
22-45718518-G-T		Benign (Nov 10, 2018)	link
22-45729448-T-C	Inborn genetic diseases	Uncertain significance (Jan 03, 2022)	link
22-45729600-G-T		Likely benign (-)	link
22-45738744-C-T		Uncertain significance (Jul 22, 2016)	link
22-45738783-A-AT		Uncertain significance (Oct 10, 2016)	link
22-45738814-C-T		Likely benign (Jan 01, 2021)	link
22-45739053-G-A		Benign (Nov 10, 2018)	link

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ATXN10	protein_coding	protein_coding	ENST00000252934	11	173510

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000345	0.998	125715	0	33	125748	0.000131

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.325	270	255	1.06	0.0000135	3127
Missense in Polyphen		79	75.702	1.0436		986
Synonymous	0.0366	100	100	0.995	0.00000537	929
Loss of Function	2.69	10	24.3	0.411	0.00000130	278

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000427	0.000427
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000132	0.000132
Middle Eastern	0.000163	0.000163
South Asian	0.000163	0.000163
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

Function: FUNCTION: Necessary for the survival of cerebellar neurons. Induces neuritogenesis by activating the Ras-MAP kinase pathway. May play a role in the maintenance of a critical intracellular glycosylation level and homeostasis. {ECO:0000250}.;
Disease: DISEASE: Note=Defects in ATXN1 may be a cause of nephronophthisis a chronic tubulo-interstitial nephropathy that leads to anemia, polyuria, polydipsia, isosthenuria and death in uremia. {ECO:0000269|PubMed:21565611}.;

Recessive Scores

pRec: 0.162

Intolerance Scores

loftool: 0.248
rvis_EVS: -1.02
rvis_percentile_EVS: 7.94

Haploinsufficiency Scores

pHI: 0.162
hipred: N
hipred_score: 0.474
ghis: 0.651

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: S
essential_gene_gene_trap: E
gene_indispensability_pred: E
gene_indispensability_score: 0.629

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Atxn10
Phenotype: skeleton phenotype; 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);

Gene ontology

Biological process: nervous system development;neuron projection development;cilium assembly;protein homotrimerization
Cellular component: extracellular space;cytoplasm;cytosol;plasma membrane;membrane;dendrite;neuronal cell body;perinuclear region of cytoplasm
Molecular function: protein binding;enzyme binding;identical protein binding