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NM_004425.4(ECM1):c.507del (p.Arg171fs) AND ECM1-related disorder

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jul 18, 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:
RCV003401118.4

Allele description [Variation Report for NM_004425.4(ECM1):c.507del (p.Arg171fs)]

NM_004425.4(ECM1):c.507del (p.Arg171fs)

Gene:
ECM1:extracellular matrix protein 1 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
1q21.2
Genomic location:
Preferred name:
NM_004425.4(ECM1):c.507del (p.Arg171fs)
Other names:
NP_004416.2:p.Pro169ProfsTer8
HGVS:
  • NC_000001.11:g.150510997del
  • NG_012062.1:g.7987del
  • NM_001202858.2:c.588del
  • NM_004425.4:c.507delMANE SELECT
  • NM_022664.3:c.507del
  • NP_001189787.1:p.Arg198fs
  • NP_004416.2:p.Arg171fs
  • NP_073155.2:p.Arg171fs
  • NC_000001.10:g.150483473del
  • NM_004425.3:c.507delT
Protein change:
R171fs
Links:
OMIM: 602201.0004; dbSNP: rs869025565
NCBI 1000 Genomes Browser:
rs869025565
Molecular consequence:
  • NM_001202858.2:c.588del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_004425.4:c.507del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_022664.3:c.507del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:
ECM1-related disorder
Synonyms:
ECM1-related condition
Identifiers:

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004104840PreventionGenetics, part of Exact Sciences
criteria provided, single submitter

(ACMG Guidelines, 2015)		Pathogenic
(Jul 18, 2023) 		germlineclinical testing

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

Help

Summary from all submissions

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

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From PreventionGenetics, part of Exact Sciences, SCV004104840.1

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

Description

The ECM1 c.507delT variant is predicted to result in a frameshift and premature protein termination (p.Arg171Glyfs*7). This variant has been reported in the homozygous state in individuals with lipoid proteinosis (Hamada et al. 2003. PubMed ID: 12603844; Samdani et al. 2010. PubMed ID: 21886756; Oguz Akarsu et al. 2018. PubMed ID: 28434238). This variant is reported in 0.0040% of alleles in individuals of African descent in gnomAD (http://gnomad.broadinstitute.org/variant/1-150483472-CT-C). Frameshift variants in ECM1 are expected to be pathogenic. This variant is interpreted as pathogenic.

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

Last Updated: Nov 10, 2024