NM_033056.4(PCDH15):c.5371CCT[1] (p.Pro1792_Pro1793del) AND not provided

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Jul 19, 2022
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV001813855.3

Allele description [Variation Report for NM_033056.4(PCDH15):c.5371CCT[1] (p.Pro1792_Pro1793del)]

NM_033056.4(PCDH15):c.5371CCT[1] (p.Pro1792_Pro1793del)

Gene:

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

Variant type:

Microsatellite

Cytogenetic location:

10q21.1

Genomic location:

Preferred name:

NM_033056.4(PCDH15):c.5371CCT[1] (p.Pro1792_Pro1793del)

HGVS:

NC_000010.11:g.53822348GGA[1]
NG_009191.3:g.1811828CCT[1]
NM_001142763.2:c.5392CCT[1]
NM_001142764.2:c.5377CCT[1]
NM_001142765.2:c.5164CCT[1]
NM_001142766.2:c.5362CCT[1]
NM_001142767.2:c.5251CCT[1]
NM_001142768.2:c.5311CCT[1]
NM_001142769.3:c.4409+2784_4409+2789del
NM_001142770.3:c.4373+2784_4373+2789del
NM_001142771.2:c.4388+2784_4388+2789del
NM_001142772.2:c.4373+2784_4373+2789del
NM_001142773.2:c.5302CCT[1]
NM_001354404.2:c.5305CCT[1]
NM_001354411.2:c.4388+5041_4388+5046del
NM_001354420.2:c.4367+5041_4367+5046del
NM_001354429.2:c.4368-4339_4368-4334del
NM_001384140.1:c.4368-2122_4368-2117delMANE SELECT
NM_033056.4:c.5371CCT[1]
NP_001136235.1:p.Pro1799_Pro1800del
NP_001136236.1:p.Pro1794_Pro1795del
NP_001136237.1:p.Pro1723_Pro1724del
NP_001136238.1:p.Pro1789_Pro1790del
NP_001136239.1:p.Pro1752_Pro1753del
NP_001136240.1:p.Pro1772_Pro1773del
NP_001136245.1:p.Pro1769_Pro1770del
NP_001341333.1:p.Pro1770_Pro1771del
NP_149045.3:p.Pro1792_Pro1793del
NC_000010.10:g.55582107_55582112del
NC_000010.10:g.55582108GGA[1]
NM_033056.3:c.5374_5379del
NM_033056.4:c.5374_5379del

Links:

dbSNP: rs978342737

NCBI 1000 Genomes Browser:

rs978342737

Molecular consequence:

NM_001142763.2:c.5392CCT[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001142764.2:c.5377CCT[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001142765.2:c.5164CCT[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001142766.2:c.5362CCT[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001142767.2:c.5251CCT[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001142768.2:c.5311CCT[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001142773.2:c.5302CCT[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001354404.2:c.5305CCT[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_033056.4:c.5371CCT[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001142769.3:c.4409+2784_4409+2789del - intron variant - [Sequence Ontology: SO:0001627]
NM_001142770.3:c.4373+2784_4373+2789del - intron variant - [Sequence Ontology: SO:0001627]
NM_001142771.2:c.4388+2784_4388+2789del - intron variant - [Sequence Ontology: SO:0001627]
NM_001142772.2:c.4373+2784_4373+2789del - intron variant - [Sequence Ontology: SO:0001627]
NM_001354411.2:c.4388+5041_4388+5046del - intron variant - [Sequence Ontology: SO:0001627]
NM_001354420.2:c.4367+5041_4367+5046del - intron variant - [Sequence Ontology: SO:0001627]
NM_001354429.2:c.4368-4339_4368-4334del - intron variant - [Sequence Ontology: SO:0001627]
NM_001384140.1:c.4368-2122_4368-2117del - 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
SCV002061066	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Uncertain significance (Jan 10, 2022)	germline	clinical testing	Citation Link,
SCV003471623	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jul 19, 2022)	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

SCV002061066

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Uncertain significance
(Jan 10, 2022)

germline

clinical testing

Citation Link,

SCV003471623

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jul 19, 2022)

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
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

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):240-242.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From GeneDx, SCV002061066.2

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

Description

Not observed at significant frequency in large population cohorts (gnomAD); In-frame deletion of 2 amino acids in a non-repeat region; In silico analysis supports that this variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge; This variant is associated with the following publications: (PMID: 15537665)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Invitae, SCV003471623.1

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

Description

This variant, c.5374_5379del, results in the deletion of 2 amino acid(s) of the PCDH15 protein (p.Pro1792_Pro1793del), but otherwise preserves the integrity of the reading frame. This variant is present in population databases (no rsID available, gnomAD 0.007%). This variant has not been reported in the literature in individuals affected with PCDH15-related conditions. ClinVar contains an entry for this variant (Variation ID: 1334341). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of 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: Dec 24, 2023

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