NM_018075.5(ANO10):c.1A>G (p.Met1Val) AND Autosomal recessive spinocerebellar ataxia 10

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Mar 31, 2022
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV002471801.1

Allele description [Variation Report for NM_018075.5(ANO10):c.1A>G (p.Met1Val)]

NM_018075.5(ANO10):c.1A>G (p.Met1Val)

Gene:

ANO10:anoctamin 10 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

3p21.33

Genomic location:

Preferred name:

NM_018075.5(ANO10):c.1A>G (p.Met1Val)

HGVS:

NC_000003.12:g.43605852T>C
NG_028216.2:g.90743A>G
NM_001204831.3:c.1A>G
NM_001204832.3:c.1A>G
NM_001204833.3:c.1A>G
NM_001204834.3:c.1A>G
NM_001346463.2:c.1A>G
NM_001346464.2:c.1A>G
NM_001346465.2:c.1A>G
NM_001346466.2:c.1A>G
NM_001346467.2:c.1A>G
NM_001346468.2:c.1A>G
NM_001346469.2:c.1A>G
NM_018075.5:c.1A>GMANE SELECT
NP_001191760.1:p.Met1Val
NP_001191761.1:p.Met1Val
NP_001191762.1:p.Met1Val
NP_001191763.1:p.Met1Val
NP_001333392.1:p.Met1Val
NP_001333393.1:p.Met1Val
NP_001333394.1:p.Met1Val
NP_001333395.1:p.Met1Val
NP_001333396.1:p.Met1Val
NP_001333397.1:p.Met1Val
NP_001333398.1:p.Met1Val
NP_060545.3:p.Met1Val
NC_000003.11:g.43647344T>C
NM_018075.4:c.1A>G

Protein change:

M1V

Molecular consequence:

NM_001204831.3:c.1A>G - initiator_codon_variant - [Sequence Ontology: SO:0001582]
NM_001204832.3:c.1A>G - initiator_codon_variant - [Sequence Ontology: SO:0001582]
NM_001204833.3:c.1A>G - initiator_codon_variant - [Sequence Ontology: SO:0001582]
NM_001204834.3:c.1A>G - initiator_codon_variant - [Sequence Ontology: SO:0001582]
NM_001346463.2:c.1A>G - initiator_codon_variant - [Sequence Ontology: SO:0001582]
NM_001346464.2:c.1A>G - initiator_codon_variant - [Sequence Ontology: SO:0001582]
NM_001346465.2:c.1A>G - initiator_codon_variant - [Sequence Ontology: SO:0001582]
NM_001346466.2:c.1A>G - initiator_codon_variant - [Sequence Ontology: SO:0001582]
NM_001346467.2:c.1A>G - initiator_codon_variant - [Sequence Ontology: SO:0001582]
NM_001346468.2:c.1A>G - initiator_codon_variant - [Sequence Ontology: SO:0001582]
NM_001346469.2:c.1A>G - initiator_codon_variant - [Sequence Ontology: SO:0001582]
NM_018075.5:c.1A>G - initiator_codon_variant - [Sequence Ontology: SO:0001582]
NM_001204831.3:c.1A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001204832.3:c.1A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001204833.3:c.1A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001204834.3:c.1A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001346463.2:c.1A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001346464.2:c.1A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001346465.2:c.1A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001346466.2:c.1A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001346467.2:c.1A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001346468.2:c.1A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001346469.2:c.1A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_018075.5:c.1A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Autosomal recessive spinocerebellar ataxia 10
Identifiers:: MONDO: MONDO:0013392; MedGen: C3150998; Orphanet: 284289; OMIM: 613728

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002766750	Victorian Clinical Genetics Services, Murdoch Childrens Research Institute See additional submitters Shariant Australia, Australian Genomics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Mar 31, 2022)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 30078120, 25741868

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002766750

Victorian Clinical Genetics Services, Murdoch Childrens Research Institute

See additional submitters

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Mar 31, 2022)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

High Degree of Genetic Heterogeneity for Hereditary Cerebellar Ataxias in Australia.

Kang C, Liang C, Ahmad KE, Gu Y, Siow SF, Colebatch JG, Whyte S, Ng K, Cremer PD, Corbett AJ, Davis RL, Roscioli T, Cowley MJ, Park JS, Sue CM, Kumar KR.

Cerebellum. 2019 Feb;18(1):137-146. doi: 10.1007/s12311-018-0969-7.

PubMed [citation]

PMID:: 30078120

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee.

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Victorian Clinical Genetics Services, Murdoch Childrens Research Institute, SCV002766750.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Likely pathogenic. Following criteria are met: 0102 - Loss of function is a known mechanism of disease in this gene and is associated with spinocerebellar ataxia 10 (MIM#613728). (I) 0106 - This gene is associated with autosomal recessive disease. (I) 0206 - Variant is predicted to result in a loss of the canonical translation initiation codon (ATG). (SP) 0251 - This variant is heterozygous. (I) 0301 - Variant is absent from gnomAD (both v2 and v3). (SP) 0311 - Three alternative nucleotide changes at the initiation codon, are present in gnomAD (v2) at a frequency of 0.00002 (highest allele count: 0 heterozygotes, 1 homozygote). (I) 0704 - Another start loss variant comparable to the one identified in this case has limited previous evidence for pathogenicity. The alternative change, c.2T>C, has been reported as likely pathogenic and pathogenic in ClinVar. (SP) 0803 - This variant has limited previous evidence of pathogenicity in an individual. This variant has been reported in a homozygous individual with hereditary cerebellar ataxias (PMID: 30078120). (SP) 0905 - No published segregation evidence has been identified for this variant. (I) 1007 - No published functional evidence has been identified for this variant. (I) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 3, 2023

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