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NC_000019.9:g.(?_6361586)_(8212364_?)del AND Mucolipidosis type IV

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Aug 7, 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:
RCV003109715.4

Allele description [Variation Report for NC_000019.9:g.(?_6361586)_(8212364_?)del]

NC_000019.9:g.(?_6361586)_(8212364_?)del

Genes:
  • CCL25:C-C motif chemokine ligand 25 [Gene - OMIM - HGNC]
  • CLEC4G:C-type lectin domain family 4 member G [Gene - OMIM - HGNC]
  • CLEC4M:C-type lectin domain family 4 member M [Gene - OMIM - HGNC]
  • CD209:CD209 molecule [Gene - OMIM - HGNC]
  • CD70:CD70 molecule [Gene - OMIM - HGNC]
  • DENND1C:DENN domain containing 1C [Gene - OMIM - HGNC]
  • ELAVL1:ELAV like RNA binding protein 1 [Gene - OMIM - HGNC]
  • FCER2:Fc epsilon receptor II [Gene - OMIM - HGNC]
  • GPR108:G protein-coupled receptor 108 [Gene - OMIM - HGNC]
  • KHSRP:KH-type splicing regulatory protein [Gene - OMIM - HGNC]
  • PET100:PET100 cytochrome c oxidase chaperone [Gene - OMIM - HGNC]
  • PCP2:Purkinje cell protein 2 [Gene - OMIM - HGNC]
  • ARHGEF18:Rho/Rac guanine nucleotide exchange factor 18 [Gene - OMIM - HGNC]
  • SH2D3A:SH2 domain containing 3A [Gene - OMIM - HGNC]
  • TNFSF14:TNF superfamily member 14 [Gene - OMIM - HGNC]
  • TNFSF9:TNF superfamily member 9 [Gene - OMIM - HGNC]
  • XAB2:XPA binding protein 2 [Gene - OMIM - HGNC]
  • ADGRE1:adhesion G protein-coupled receptor E1 [Gene - OMIM - HGNC]
  • ALKBH7:alkB homolog 7 [Gene - OMIM - HGNC]
  • CAMSAP3:calmodulin regulated spectrin associated protein family member 3 [Gene - OMIM - HGNC]
  • CLPP:caseinolytic mitochondrial matrix peptidase proteolytic subunit [Gene - OMIM - HGNC]
  • C3:complement C3 [Gene - OMIM - HGNC]
  • CTXN1:cortexin 1 [Gene - OMIM - HGNC]
  • CRB3:crumbs cell polarity complex component 3 [Gene - OMIM - HGNC]
  • EVI5L:ecotropic viral integration site 5 like [Gene - HGNC]
  • FBN3:fibrillin 3 [Gene - OMIM - HGNC]
  • GTF2F1:general transcription factor IIF subunit 1 [Gene - OMIM - HGNC]
  • INSR:insulin receptor [Gene - OMIM - HGNC]
  • LRRC8E:leucine rich repeat containing 8 VRAC subunit E [Gene - OMIM - HGNC]
  • MCEMP1:mast cell expressed membrane protein 1 [Gene - OMIM - HGNC]
  • MBD3L2:methyl-CpG binding domain protein 3 like 2 [Gene - OMIM - HGNC]
  • MBD3L3:methyl-CpG binding domain protein 3 like 3 [Gene - HGNC]
  • MBD3L4:methyl-CpG binding domain protein 3 like 4 [Gene - HGNC]
  • MBD3L5:methyl-CpG binding domain protein 3 like 5 [Gene - HGNC]
  • MAP2K7:mitogen-activated protein kinase kinase 7 [Gene - OMIM - HGNC]
  • MCOLN1:mucolipin TRP cation channel 1 [Gene - OMIM - HGNC]
  • PNPLA6:patatin like phospholipase domain containing 6 [Gene - OMIM - HGNC]
  • PEX11G:peroxisomal biogenesis factor 11 gamma [Gene - OMIM - HGNC]
  • PSPN:persephin [Gene - OMIM - HGNC]
  • RETN:resistin [Gene - OMIM - HGNC]
  • SNAPC2:small nuclear RNA activating complex polypeptide 2 [Gene - OMIM - HGNC]
  • SLC25A23:solute carrier family 25 member 23 [Gene - OMIM - HGNC]
  • SLC25A41:solute carrier family 25 member 41 [Gene - OMIM - HGNC]
  • SAXO5:stabilizer of axonemal microtubules 5 [Gene - HGNC]
  • STXBP2:syntaxin binding protein 2 [Gene - OMIM - HGNC]
  • TRIP10:thyroid hormone receptor interactor 10 [Gene - OMIM - HGNC]
  • TRAPPC5:trafficking protein particle complex subunit 5 [Gene - HGNC]
  • TGFBR3L:transforming growth factor beta receptor 3 like [Gene - HGNC]
  • TIMM44:translocase of inner mitochondrial membrane 44 [Gene - OMIM - HGNC]
  • TUBB4A:tubulin beta 4A class IVa [Gene - OMIM - HGNC]
  • VAV1:vav guanine nucleotide exchange factor 1 [Gene - OMIM - HGNC]
  • ZNF358:zinc finger protein 358 [Gene - OMIM - HGNC]
  • ZNF557:zinc finger protein 557 [Gene - HGNC]
Variant type:
Deletion
Cytogenetic location:
19p13.3-13.2
Genomic location:
Chr19: 6361586 - 8212364 (on Assembly GRCh37)
Preferred name:
NC_000019.9:g.(?_6361586)_(8212364_?)del
HGVS:
NC_000019.9:g.(?_6361586)_(8212364_?)del

Condition(s)

Name:
Mucolipidosis type IV (ML4)
Synonyms:
ML IV; Mucolipidosis type 4; ML 4
Identifiers:
MONDO: MONDO:0009653; MedGen: C0238286; Orphanet: 578; OMIM: 252650

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003791710Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Aug 7, 2022) 		germlineclinical testing

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Mucolipidosis type IV is caused by mutations in a gene encoding a novel transient receptor potential channel.

Sun M, Goldin E, Stahl S, Falardeau JL, Kennedy JC, Acierno JS Jr, Bove C, Kaneski CR, Nagle J, Bromley MC, Colman M, Schiffmann R, Slaugenhaupt SA.

Hum Mol Genet. 2000 Oct 12;9(17):2471-8.

PubMed [citation]
PMID:
11030752

Mucolipidosis type IV: novel MCOLN1 mutations in Jewish and non-Jewish patients and the frequency of the disease in the Ashkenazi Jewish population.

Bargal R, Avidan N, Olender T, Ben Asher E, Zeigler M, Raas-Rothschild A, Frumkin A, Ben-Yoseph O, Friedlender Y, Lancet D, Bach G.

Hum Mutat. 2001 May;17(5):397-402.

PubMed [citation]
PMID:
11317355
See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003791710.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

A gross deletion of the genomic region encompassing the full coding sequence of the MCOLN1 gene has been identified. Loss-of-function variants in MCOLN1 are known to be pathogenic (PMID: 11030752, 11317355). 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 MCOLN1-related conditions. For these reasons, this variant has been classified as Pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024