NC_000005.9:g.(?_218471)_(1895829_?)del AND Parkinsonism-dystonia, infantile

This record was updated by the submitter. Please see the current version.

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Oct 2, 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:: RCV003120784.9

Allele description

NC_000005.9:g.(?_218471)_(1895829_?)del

Genes:

CLPTM1L:CLPTM1 like [Gene - OMIM - HGNC]
EXOC3-AS1:EXOC3 antisense RNA 1 [Gene - HGNC]
NDUFS6:NADH:ubiquinone oxidoreductase subunit S6 [Gene - OMIM - HGNC]
NKD2:NKD inhibitor of WNT signaling pathway 2 [Gene - OMIM - HGNC]
AHRR:aryl hydrocarbon receptor repressor [Gene - OMIM - HGNC]
BRD9:bromodomain containing 9 [Gene - OMIM - HGNC]
CEP72:centrosomal protein 72 [Gene - OMIM - HGNC]
EXOC3:exocyst complex component 3 [Gene - OMIM - HGNC]
IRX4:iroquois homeobox 4 [Gene - OMIM - HGNC]
LPCAT1:lysophosphatidylcholine acyltransferase 1 [Gene - OMIM - HGNC]
MRPL36:mitochondrial ribosomal protein L36 [Gene - OMIM - HGNC]
PDCD6:programmed cell death 6 [Gene - OMIM - HGNC]
SLC12A7:solute carrier family 12 member 7 [Gene - OMIM - HGNC]
SLC6A18:solute carrier family 6 member 18 [Gene - OMIM - HGNC]
SLC6A19:solute carrier family 6 member 19 [Gene - OMIM - HGNC]
SLC6A3:solute carrier family 6 member 3 [Gene - OMIM - HGNC]
SLC9A3:solute carrier family 9 member A3 [Gene - OMIM - HGNC]
SDHA:succinate dehydrogenase complex flavoprotein subunit A [Gene - OMIM - HGNC]
TERT:telomerase reverse transcriptase [Gene - OMIM - HGNC]
TRIP13:thyroid hormone receptor interactor 13 [Gene - OMIM - HGNC]
TPPP:tubulin polymerization promoting protein [Gene - OMIM - HGNC]
ZDHHC11:zinc finger DHHC-type containing 11 [Gene - HGNC]
ZDHHC11B:zinc finger DHHC-type containing 11B [Gene - HGNC]

Variant type:

Deletion

Cytogenetic location:

5p15.33

Genomic location:

Chr5: 218471 - 1895829 (on Assembly GRCh37)

Preferred name:

NC_000005.9:g.(?_218471)_(1895829_?)del

HGVS:

NC_000005.9:g.(?_218471)_(1895829_?)del

Condition(s)

Name:: Parkinsonism-dystonia, infantile
Identifiers:: MONDO: MONDO:0013150; MedGen: C2751067; Orphanet: 238455; OMIM: PS613135

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003791001	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Oct 2, 2022)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 21112253, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003791001

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Oct 2, 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	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Clinical and molecular characterisation of hereditary dopamine transporter deficiency syndrome: an observational cohort and experimental study.

Kurian MA, Li Y, Zhen J, Meyer E, Hai N, Christen HJ, Hoffmann GF, Jardine P, von Moers A, Mordekar SR, O'Callaghan F, Wassmer E, Wraige E, Dietrich C, Lewis T, Hyland K, Heales S Jr, Sanger T, Gissen P, Assmann BE, Reith ME, Maher ER.

Lancet Neurol. 2011 Jan;10(1):54-62. doi: 10.1016/S1474-4422(10)70269-6. Epub 2010 Nov 25.

PubMed [citation]

PMID:: 21112253
PMCID:: PMC3002401

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV003791001.2

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

Description

A gross deletion of the genomic region encompassing the full coding sequence of the SLC6A3 gene has been identified. Loss-of-function variants in SLC6A3 are known to be pathogenic (PMID: 21112253). The boundaries of this event are unknown as they extend beyond the assayed region for this gene and therefore may encompass additional genes. This variant has not been reported in the literature in individuals affected with SLC6A3-related conditions. For these reasons, this variant has been classified as Pathogenic.

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

Last Updated: Sep 16, 2024

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