NM_001142864.4(PIEZO1):c.5072_5074del (p.Cys1691del) AND Lymphatic malformation 6

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Sep 23, 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:: RCV003458285.1

Allele description [Variation Report for NM_001142864.4(PIEZO1):c.5072_5074del (p.Cys1691del)]

NM_001142864.4(PIEZO1):c.5072_5074del (p.Cys1691del)

Gene:

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.5072_5074del (p.Cys1691del)

HGVS:

NC_000016.10:g.88721950_88721952del
NG_042229.1:g.68271_68273del
NM_001142864.4:c.5072_5074delMANE SELECT
NM_014745.1:c.3612_3614delCTG
NP_001136336.2:p.Cys1691del
NP_055560.1:p.Cys1205del
LRG_1137t1:c.5072_5074del
LRG_1137:g.68271_68273del
LRG_1137p1:p.Cys1691del
NC_000016.9:g.88788358_88788360del

Protein change:

C1205del

Molecular consequence:

NM_001142864.4:c.5072_5074del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_014745.1:c.3612_3614delCTG - inframe_indel - [Sequence Ontology: SO:0001820]

Condition(s)

Name:: Lymphatic malformation 6 (LMPHM6)
Synonyms:: GENERALIZED LYMPHATIC DYSPLASIA OF FOTIOU; Lymphedema, hereditary, III
Identifiers:: MONDO: MONDO:0014797; MedGen: C4225184; OMIM: 616843

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Homo sapiens SURP and G patch domain containing 1 (SUGP1), mRNA
Homo sapiens SURP and G patch domain containing 1 (SUGP1), mRNA
gi|33469963|ref|NM_172231.2|

Nucleotide
Mus musculus fibroblast growth factor 18 (Fgf18), transcript variant 1, mRNA
Mus musculus fibroblast growth factor 18 (Fgf18), transcript variant 1, mRNA
gi|474451730|ref|NM_008005.2|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004177057	Clinical Genomics Laboratory, Washington University in St. Louis	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Sep 23, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004177057

Clinical Genomics Laboratory, Washington University in St. Louis

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Sep 23, 2023)

germline

clinical testing

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

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

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 Clinical Genomics Laboratory, Washington University in St. Louis, SCV004177057.1

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

Description

The PIEZO1 c.5072_5074del (p.Cys1691del) variant was identified at near heterozygous allelic fraction and to our knowledge, it has not been reported in the medical literature. This variant is absent from the general population (gnomAD v.3.1.2), indicating it is not a common variant. Computational predictors indicate that this variant does not impact PIEZO1 function. PIEZO1 c.5072_5074del (p.Cys1691del) is predicted to cause a change in the length of the protein due to an in-frame deletion of one amino acid in a non-repeat region. Due to limited information, and based on ACMG/AMP guidelines for variant interpretation (Richards S et al., PMID: 25741868), this variant is classified as being of uncertain significance at this time.

#	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 28, 2024

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