VCV000030886.4 - ClinVar

NM_018713.3(SLC30A10):c.266T>C (p.Leu89Pro)

Germline

Classification

no assertion criteria provided. Learn more about how ClinVar calculates review status.

Pathogenic

1 out of 2 submissions contributed to this classification

The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_018713.3(SLC30A10):c.266T>C (p.Leu89Pro)

Variation ID: 30886 Accession: VCV000030886.4

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 1q41 1: 219928175 (GRCh38) [ NCBI UCSC ] 1: 220101517 (GRCh37) [ NCBI UCSC ]

Timeline in ClinVar

	First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.	Last submission Help The date of the most recent submission for each type of classification for this variant.	Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline	Apr 4, 2013	Oct 1, 2022	Mar 9, 2012

HGVS

Nucleotide	Protein	Molecular consequence
NM_018713.3:c.266T>C MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_061183.2:p.Leu89Pro	missense
NM_001376929.1:c.452-1070T>C		intron variant
NR_046437.2:n.383T>C		non-coding transcript variant
NC_000001.11:g.219928175A>G
NC_000001.10:g.220101517A>G
NG_032153.2:g.5477T>C
	Q6XR72:p.Leu89Pro

... more HGVS ... less HGVS

Protein change

L89P

Other names

Canonical SPDI

NC_000001.11:219928174:A:G

Global minor allele frequency (GMAF) Help The global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.

Allele frequency Help The frequency of the allele represented by this VCV record.

Links

dbSNP: rs281860284 ClinGen: CA342757 UniProtKB: Q6XR72#VAR_072573 OMIM: 611146.0002 VarSome

Genes

Gene	OMIM	ClinGen Gene Dosage Sensitivity Curation		Variation Viewer Help Links to Variation Viewer, a genome browser to view variation data from NCBI databases.	Related variants
Gene	OMIM	HI score Help The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.	TS score Help The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.		Within gene Help The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants.	All Help The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene.
SLC30A10		Gene associated with autosomal recessive phenotype	No evidence available	GRCh38 GRCh37	314	358

Conditions - Germline

Condition Help The condition for this variant-condition (RCV) record in ClinVar.	Classification Help The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions)	Review status Help The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status.	Last evaluated Help The most recent date that a submitter evaluated this variant for the condition.	Variation/condition record Help The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page.
Hypermanganesemia with dystonia, polycythemia, and cirrhosis	Pathogenic (2)	no assertion criteria provided	Mar 9, 2012	RCV000023871.8

Submissions - Germline

Classification Help The submitted germline classification for each SCV record. (Last evaluated)	Review status Help Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria)	Condition Help The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant.	Submitter Help The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar.	Expand all rows Collapse all rows Help This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.
Pathogenic (Mar 09, 2012) C Contributing to aggregate classification	no assertion criteria provided	HYPERMANGANESEMIA WITH DYSTONIA 1	OMIM Accession: SCV000045162.5 First in ClinVar: Apr 04, 2013 Last updated: Jul 07, 2021	Publications: PubMed (1) PubMed: 22341972 Observation: 1 Collection method: literature only Allele origin: germline Affected status: not provided more Observation 1 Collection method: literature only Allele origin: germline Affected status: not provided Comment on evidence: In 3 Arab sisters, born of consanguineous parents, with hypermanganesemia with dystonia-1 (HMNDYT1; 613280), Tuschl et al. (2012) identified a homozygous 266T-C transition in exon … (more) In 3 Arab sisters, born of consanguineous parents, with hypermanganesemia with dystonia-1 (HMNDYT1; 613280), Tuschl et al. (2012) identified a homozygous 266T-C transition in exon 1 of the SLC30A10 gene, resulting in a leu89-to-pro (L89P) substitution in a highly conserved residue. The mutation was not found in 200 controls. In vitro functional expression studies in a yeast strain lacking a manganese transporter demonstrated that the L89P mutant protein was nonfunctional. (less)

not provided (-) N Not contributing to aggregate classification	no classification provided	Hypermanganesemia with dystonia, polycythemia, and cirrhosis	GeneReviews Accession: SCV000054645.2 First in ClinVar: Apr 04, 2013 Last updated: Oct 01, 2022	Publications: PubMed (1) PubMed: 22934317 BookShelf: NBK100241 BookShelf: NBK100241 Observation: 1 Collection method: literature only Allele origin: unknown Affected status: not provided Observation 1 Collection method: literature only Allele origin: unknown Affected status: not provided

Citations for germline classification of this variant

Title	Author	Journal	Year	Link
Hypermanganesemia with Dystonia 1.	Adam MP	-	2021	PMID: 22934317
Syndrome of hepatic cirrhosis, dystonia, polycythemia, and hypermanganesemia caused by mutations in SLC30A10, a manganese transporter in man.	Tuschl K	American journal of human genetics	2012	PMID: 22341972

Text-mined citations for rs281860284 ...

These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Apr 13, 2026