NM_018713.3(SLC30A10):c.1235del (p.Gln412fs) AND Hypermanganesemia with dystonia, polycythemia, and cirrhosis

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Mar 9, 2012
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

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:: RCV000023874.6

Allele description [Variation Report for NM_018713.3(SLC30A10):c.1235del (p.Gln412fs)]

NM_018713.3(SLC30A10):c.1235del (p.Gln412fs)

Gene:

SLC30A10:solute carrier family 30 member 10 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

1q41

Genomic location:

Preferred name:

NM_018713.3(SLC30A10):c.1235del (p.Gln412fs)

HGVS:

NC_000001.11:g.219915672del
NG_032153.2:g.17980del
NM_001376929.1:c.1046del
NM_018713.3:c.1235delMANE SELECT
NP_001363858.1:p.Gln349fs
NP_061183.2:p.Gln412fs
NC_000001.10:g.220089014del
NM_018713.2:c.1235delA
NR_046437.2:n.1390del
NR_165031.1:n.1127del

Protein change:

Q349fs

Links:

OMIM: 611146.0005; dbSNP: rs281860292

NCBI 1000 Genomes Browser:

rs281860292

Molecular consequence:

NM_001376929.1:c.1046del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_018713.3:c.1235del - frameshift variant - [Sequence Ontology: SO:0001589]
NR_046437.2:n.1390del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_165031.1:n.1127del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Hypermanganesemia with dystonia, polycythemia, and cirrhosis (HMNDYT1)
Synonyms:: Hypermanganesemia with dystonia 1; Hepatic Cirrhosis, Dystonia, Polycythemia and Hypermanganesemia; Dystonia/Parkinsonism, Hypermanganesemia, Polycythemia, and Chronic Liver Disease; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0013208; MedGen: C2750442; Orphanet: 309854; OMIM: 613280

Recent activity

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fibropellin-1-like isoform X11 [Patiria miniata]
fibropellin-1-like isoform X11 [Patiria miniata]
gi|1944835312|ref|XP_038046978.1|

Protein
fibropellin-1-like isoform X15 [Patiria miniata]
fibropellin-1-like isoform X15 [Patiria miniata]
gi|1944835332|ref|XP_038046982.1|

Protein
fibropellin-1-like isoform X17 [Patiria miniata]
fibropellin-1-like isoform X17 [Patiria miniata]
gi|1944835342|ref|XP_038046984.1|

Protein
LOW QUALITY PROTEIN: nidogen-1-like [Acanthaster planci]
LOW QUALITY PROTEIN: nidogen-1-like [Acanthaster planci]
gi|1229138369|ref|XP_022081243.1|

Protein
Macrocentrus sp. MD-1997 28S ribosomal RNA gene, partial sequence
Macrocentrus sp. MD-1997 28S ribosomal RNA gene, partial sequence
gi|3859814|gb|AF029135.1|AF029135

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000045165	OMIM	no assertion criteria provided	Pathogenic (Mar 9, 2012)	germline	literature only	PubMed (1) [See all records that cite this PMID]
SCV000054644	GeneReviews	no classification provided	not provided	unknown	literature only	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000045165

OMIM

no assertion criteria provided

Pathogenic
(Mar 9, 2012)

germline

literature only

PubMed (1)
[See all records that cite this PMID]

SCV000054644

GeneReviews

no classification provided

not provided

unknown

literature only

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	unknown	not provided	not provided	not provided	not provided	not provided	not provided	literature only
not provided	germline	not provided	not provided	not provided	not provided	not provided	not provided	literature only

Citations

PubMed

Mutations in SLC30A10 cause parkinsonism and dystonia with hypermanganesemia, polycythemia, and chronic liver disease.

Quadri M, Federico A, Zhao T, Breedveld GJ, Battisti C, Delnooz C, Severijnen LA, Di Toro Mammarella L, Mignarri A, Monti L, Sanna A, Lu P, Punzo F, Cossu G, Willemsen R, Rasi F, Oostra BA, van de Warrenburg BP, Bonifati V.

Am J Hum Genet. 2012 Mar 9;90(3):467-77. doi: 10.1016/j.ajhg.2012.01.017. Epub 2012 Feb 16.

PubMed [citation]

PMID:: 22341971
PMCID:: PMC3309204

Hypermanganesemia with Dystonia 1.

Tuschl K, Clayton PT, Gospe SM Jr, Mills PB.

2012 Aug 30 [updated 2021 Dec 23]. In: Adam MP, Feldman J, Mirzaa GM, Pagon RA, Wallace SE, Amemiya A, editors. GeneReviews(®) [Internet]. Seattle (WA): University of Washington, Seattle; 1993-2024.

PubMed [citation]

PMID:: 22934317

Details of each submission

From OMIM, SCV000045165.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	literature only	PubMed (1)

Description

In 2 Italian brothers, born of consanguineous parents, with hypermanganesemia with dystonia-1 (HMNDYT1; 613280), Quadri et al. (2012) identified a homozygous 1-bp deletion (1235delA) in exon 4 of the SLC30A10 gene, resulting in a frameshift and premature termination. The mutation was not found in the 1000 Genomes Project or Exome Variant Server databases or in 996 control chromosomes. The brothers presented at age 47 and 57 years, respectively, with parkinsonism, including gait disturbances, bradykinesia, hypomimia, rigidity, and postural instability. Both also had polycythemia, hepatomegaly, and brain MRI lesions in the basal ganglia, midbrain, thalamus, cerebellum, and corticospinal tract. One patient had a sensorimotor axonal polyneuropathy. Laboratory studies showed markedly increased manganese, increased transferrin, and decreased ferritin. Chelation therapy resulted in clinical improvement.

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

From GeneReviews, SCV000054644.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	literature only	PubMed (1)

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

Last Updated: Oct 8, 2022

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