NM_001142864.4(PIEZO1):c.1537del (p.Cys513fs) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jul 6, 2017
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:: RCV001380953.4

Allele description [Variation Report for NM_001142864.4(PIEZO1):c.1537del (p.Cys513fs)]

NM_001142864.4(PIEZO1):c.1537del (p.Cys513fs)

Genes:

HSALR1:HSP90AB1 associated lncRNA 1 [Gene - HGNC]
PIEZO1:piezo type mechanosensitive ion channel component 1 (Er blood group) [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

16q24.3

Genomic location:

Preferred name:

NM_001142864.4(PIEZO1):c.1537del (p.Cys513fs)

HGVS:

NC_000016.10:g.88736168del
NG_042229.1:g.54053del
NM_001142864.4:c.1537delMANE SELECT
NP_001136336.2:p.Cys513fs
LRG_1137t1:c.1537del
LRG_1137:g.54053del
LRG_1137p1:p.Cys513fs
NC_000016.9:g.88802576del
NC_000016.9:g.88802576delA

Protein change:

C513fs

Links:

dbSNP: rs757428415

NCBI 1000 Genomes Browser:

rs757428415

Molecular consequence:

NM_001142864.4:c.1537del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001579185	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jul 6, 2017)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 26333996, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001579185

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jul 6, 2017)

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

Novel mutations in PIEZO1 cause an autosomal recessive generalized lymphatic dysplasia with non-immune hydrops fetalis.

Fotiou E, Martin-Almedina S, Simpson MA, Lin S, Gordon K, Brice G, Atton G, Jeffery I, Rees DC, Mignot C, Vogt J, Homfray T, Snyder MP, Rockson SG, Jeffery S, Mortimer PS, Mansour S, Ostergaard P.

Nat Commun. 2015 Sep 3;6:8085. doi: 10.1038/ncomms9085. Erratum in: Nat Commun. 2019 Apr 26;10(1):1951. doi: 10.1038/s41467-019-09905-4.

PubMed [citation]

PMID:: 26333996
PMCID:: PMC4568316

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, SCV001579185.4

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

Description

For these reasons, this variant has been classified as Pathogenic. Loss-of-function variants in PIEZO1 are known to be pathogenic (PMID: 26333996). This variant has not been reported in the literature in individuals with PIEZO1-related disease. This variant is not present in population databases (ExAC no frequency). This sequence change creates a premature translational stop signal (p.Cys513Valfs*12) in the PIEZO1 gene. It is expected to result in an absent or disrupted protein product.

#	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: Feb 20, 2024

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