NM_033056.4(PCDH15):c.4864del (p.Ser1622fs) AND not specified

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jan 17, 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:: RCV003117858.3

Allele description [Variation Report for NM_033056.4(PCDH15):c.4864del (p.Ser1622fs)]

NM_033056.4(PCDH15):c.4864del (p.Ser1622fs)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

10q21.1

Genomic location:

Preferred name:

NM_033056.4(PCDH15):c.4864del (p.Ser1622fs)

HGVS:

NC_000010.11:g.53822862del
NG_009191.3:g.1811321del
NM_001142763.2:c.4885del
NM_001142764.2:c.4870del
NM_001142765.2:c.4657del
NM_001142766.2:c.4855del
NM_001142767.2:c.4744del
NM_001142768.2:c.4804del
NM_001142769.3:c.4409+2274del
NM_001142770.3:c.4373+2274del
NM_001142771.2:c.4388+2274del
NM_001142772.2:c.4373+2274del
NM_001142773.2:c.4795del
NM_001354404.2:c.4798del
NM_001354411.2:c.4388+4531del
NM_001354420.2:c.4367+4531del
NM_001354429.2:c.4367+4531del
NM_001384140.1:c.4368-2632delMANE SELECT
NM_033056.4:c.4864del
NP_001136235.1:p.Ser1629fs
NP_001136236.1:p.Ser1624fs
NP_001136237.1:p.Ser1553fs
NP_001136238.1:p.Ser1619fs
NP_001136239.1:p.Ser1582fs
NP_001136240.1:p.Ser1602fs
NP_001136245.1:p.Ser1599fs
NP_001341333.1:p.Ser1600fs
NP_149045.3:p.Ser1622fs
NC_000010.10:g.55582622del
NM_001142763.2:c.4885delA
NM_033056.3:c.4864del
NM_033056.3:c.4864delA
p.S1629fs

Protein change:

S1553fs

Links:

dbSNP: rs1393195833

NCBI 1000 Genomes Browser:

rs1393195833

Molecular consequence:

NM_001142763.2:c.4885del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001142764.2:c.4870del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001142765.2:c.4657del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001142766.2:c.4855del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001142767.2:c.4744del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001142768.2:c.4804del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001142773.2:c.4795del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354404.2:c.4798del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_033056.4:c.4864del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001142769.3:c.4409+2274del - intron variant - [Sequence Ontology: SO:0001627]
NM_001142770.3:c.4373+2274del - intron variant - [Sequence Ontology: SO:0001627]
NM_001142771.2:c.4388+2274del - intron variant - [Sequence Ontology: SO:0001627]
NM_001142772.2:c.4373+2274del - intron variant - [Sequence Ontology: SO:0001627]
NM_001354411.2:c.4388+4531del - intron variant - [Sequence Ontology: SO:0001627]
NM_001354420.2:c.4367+4531del - intron variant - [Sequence Ontology: SO:0001627]
NM_001354429.2:c.4367+4531del - intron variant - [Sequence Ontology: SO:0001627]
NM_001384140.1:c.4368-2632del - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003801224	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Uncertain significance (Jan 17, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID] Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003801224

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Uncertain significance
(Jan 17, 2023)

germline

clinical testing

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

Citation Link

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

Benefits of Exome Sequencing in Children with Suspected Isolated Hearing Loss.

Van Heurck R, Carminho-Rodrigues MT, Ranza E, Stafuzza C, Quteineh L, Gehrig C, Hammar E, Guipponi M, Abramowicz M, Senn P, Guinand N, Cao-Van H, Paoloni-Giacobino A.

Genes (Basel). 2021 Aug 20;12(8). doi:pii: 1277. 10.3390/genes12081277.

PubMed [citation]

PMID:: 34440452
PMCID:: PMC8391342

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV003801224.2

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

Description

Variant summary: PCDH15 c.4864delA (p.Ser1622AlafsX12) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay. Truncating variants in the last exon of PCDH15 have uncertain impact on protein function. The variant allele was found at a frequency of 4e-06 in 251440 control chromosomes. The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. To our knowledge, no occurrence of c.4864delA in individuals affected with Usher Syndrome Type 1F and no experimental evidence demonstrating its impact on protein function have been reported. Three clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation: likely benign (n=1), uncertain significance (n=2). Based on the evidence outlined above, the variant was classified as uncertain significance.

#	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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