NM_001384140.1(PCDH15):c.1789del (p.Ser597fs) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jun 2, 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:: RCV002820057.3

Allele description [Variation Report for NM_001384140.1(PCDH15):c.1789del (p.Ser597fs)]

NM_001384140.1(PCDH15):c.1789del (p.Ser597fs)

Gene:

PCDH15:protocadherin related 15 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

10q21.1

Genomic location:

Preferred name:

NM_001384140.1(PCDH15):c.1789del (p.Ser597fs)

HGVS:

NC_000010.11:g.54133003del
NG_009191.3:g.1501180del
NM_001142763.2:c.1804del
NM_001142764.2:c.1789del
NM_001142765.2:c.1784+20097del
NM_001142766.2:c.1789del
NM_001142767.2:c.1678del
NM_001142768.2:c.1723del
NM_001142769.3:c.1825del
NM_001142770.3:c.1789del
NM_001142771.2:c.1804del
NM_001142772.2:c.1789del
NM_001142773.2:c.1723del
NM_001354404.2:c.1723del
NM_001354411.2:c.1810del
NM_001354420.2:c.1789del
NM_001354429.2:c.1789del
NM_001354430.2:c.1789del
NM_001384140.1:c.1789delMANE SELECT
NM_033056.4:c.1789del
NP_001136235.1:p.Ser602fs
NP_001136236.1:p.Ser597fs
NP_001136238.1:p.Ser597fs
NP_001136239.1:p.Ser560fs
NP_001136240.1:p.Ser575fs
NP_001136241.1:p.Ser609fs
NP_001136242.1:p.Ser597fs
NP_001136243.1:p.Ser602fs
NP_001136244.1:p.Ser597fs
NP_001136245.1:p.Ser575fs
NP_001341333.1:p.Ser575fs
NP_001341340.1:p.Ser604fs
NP_001341349.1:p.Ser597fs
NP_001341358.1:p.Ser597fs
NP_001341359.1:p.Ser597fs
NP_001371069.1:p.Ser597fs
NP_149045.3:p.Ser597fs
NC_000010.10:g.55892763del

Protein change:

S560fs

Molecular consequence:

NM_001142763.2:c.1804del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001142764.2:c.1789del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001142766.2:c.1789del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001142767.2:c.1678del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001142768.2:c.1723del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001142769.3:c.1825del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001142770.3:c.1789del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001142771.2:c.1804del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001142772.2:c.1789del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001142773.2:c.1723del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354404.2:c.1723del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354411.2:c.1810del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354420.2:c.1789del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354429.2:c.1789del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354430.2:c.1789del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001384140.1:c.1789del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_033056.4:c.1789del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001142765.2:c.1784+20097del - intron variant - [Sequence Ontology: SO:0001627]

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
SCV003210999	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jun 2, 2022)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 11398101, 11487575, 14570705, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003210999

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jun 2, 2022)

germline

clinical testing

PubMed (4)
[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

Mutations of the protocadherin gene PCDH15 cause Usher syndrome type 1F.

Ahmed ZM, Riazuddin S, Bernstein SL, Ahmed Z, Khan S, Griffith AJ, Morell RJ, Friedman TB, Riazuddin S, Wilcox ER.

Am J Hum Genet. 2001 Jul;69(1):25-34. Epub 2001 Jun 7.

PubMed [citation]

PMID:: 11398101
PMCID:: PMC1226045

Mutations in the novel protocadherin PCDH15 cause Usher syndrome type 1F.

Alagramam KN, Yuan H, Kuehn MH, Murcia CL, Wayne S, Srisailpathy CR, Lowry RB, Knaus R, Van Laer L, Bernier FP, Schwartz S, Lee C, Morton CC, Mullins RF, Ramesh A, Van Camp G, Hageman GS, Woychik RP, Smith RJ.

Hum Mol Genet. 2001 Aug 1;10(16):1709-18. Erratum in: Hum Mol Genet 2001 Oct 15;10(22):2603. Hagemen GS [corrected to Hageman GS].

PubMed [citation]

PMID:: 11487575

See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003210999.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

This variant has not been reported in the literature in individuals affected with PCDH15-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Ser597Profs*23) in the PCDH15 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in PCDH15 are known to be pathogenic (PMID: 11398101, 11487575, 14570705). For these reasons, this variant has been classified as Pathogenic.

#	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: Sep 29, 2024

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