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NM_020533.3(MCOLN1):c.594del (p.Glu199fs) AND Mucolipidosis type IV

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Sep 21, 2023
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:
RCV001380641.5

Allele description [Variation Report for NM_020533.3(MCOLN1):c.594del (p.Glu199fs)]

NM_020533.3(MCOLN1):c.594del (p.Glu199fs)

Gene:
MCOLN1:mucolipin TRP cation channel 1 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
19p13.2
Genomic location:
Preferred name:
NM_020533.3(MCOLN1):c.594del (p.Glu199fs)
HGVS:
  • NC_000019.10:g.7527542del
  • NG_015806.1:g.9933del
  • NM_020533.3:c.594delMANE SELECT
  • NP_065394.1:p.Glu199fs
  • NC_000019.9:g.7592423del
  • NC_000019.9:g.7592428del
Protein change:
E199fs
Links:
dbSNP: rs1349755445
NCBI 1000 Genomes Browser:
rs1349755445
Molecular consequence:
  • NM_020533.3:c.594del - frameshift variant - [Sequence Ontology: SO:0001589]

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
SCV001578769Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Sep 21, 2023) 		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 Invitae, SCV001578769.5

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

Description

For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 1068939). This variant has not been reported in the literature in individuals affected with MCOLN1-related conditions. This variant is present in population databases (no rsID available, gnomAD 0.003%). This sequence change creates a premature translational stop signal (p.Glu199Serfs*39) in the MCOLN1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in MCOLN1 are known to be pathogenic (PMID: 11030752, 11317355).

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

Last Updated: Feb 28, 2024