NM_033056.4(PCDH15):c.5389C>T (p.Pro1797Ser) AND not specified

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jul 24, 2019
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:: RCV001195249.4

Allele description [Variation Report for NM_033056.4(PCDH15):c.5389C>T (p.Pro1797Ser)]

NM_033056.4(PCDH15):c.5389C>T (p.Pro1797Ser)

Gene:

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

Variant type:

single nucleotide variant

Cytogenetic location:

10q21.1

Genomic location:

Preferred name:

NM_033056.4(PCDH15):c.5389C>T (p.Pro1797Ser)

HGVS:

NC_000010.11:g.53822337G>A
NG_009191.3:g.1811846C>T
NM_001142763.2:c.5410C>T
NM_001142764.2:c.5395C>T
NM_001142765.2:c.5182C>T
NM_001142766.2:c.5380C>T
NM_001142767.2:c.5269C>T
NM_001142768.2:c.5329C>T
NM_001142769.3:c.4409+2799C>T
NM_001142770.3:c.4373+2799C>T
NM_001142771.2:c.4388+2799C>T
NM_001142772.2:c.4373+2799C>T
NM_001142773.2:c.5320C>T
NM_001354404.2:c.5323C>T
NM_001354411.2:c.4388+5056C>T
NM_001354420.2:c.4367+5056C>T
NM_001354429.2:c.4368-4324C>T
NM_001384140.1:c.4368-2107C>TMANE SELECT
NM_033056.4:c.5389C>T
NP_001136235.1:p.Pro1804Ser
NP_001136236.1:p.Pro1799Ser
NP_001136237.1:p.Pro1728Ser
NP_001136238.1:p.Pro1794Ser
NP_001136239.1:p.Pro1757Ser
NP_001136240.1:p.Pro1777Ser
NP_001136245.1:p.Pro1774Ser
NP_001341333.1:p.Pro1775Ser
NP_149045.3:p.Pro1797Ser
NC_000010.10:g.55582097G>A

Protein change:

P1728S

Links:

dbSNP: rs775203432

NCBI 1000 Genomes Browser:

rs775203432

Molecular consequence:

NM_001142769.3:c.4409+2799C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001142770.3:c.4373+2799C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001142771.2:c.4388+2799C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001142772.2:c.4373+2799C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001354411.2:c.4388+5056C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001354420.2:c.4367+5056C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001354429.2:c.4368-4324C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001384140.1:c.4368-2107C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001142763.2:c.5410C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001142764.2:c.5395C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001142765.2:c.5182C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001142766.2:c.5380C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001142767.2:c.5269C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001142768.2:c.5329C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001142773.2:c.5320C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354404.2:c.5323C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_033056.4:c.5389C>T - missense variant - [Sequence Ontology: SO:0001583]

Observations:

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
SCV001365556	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	criteria provided, single submitter (LMM Criteria)	Uncertain significance (Jul 24, 2019)	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

SCV001365556

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

criteria provided, single submitter

(LMM Criteria)

Uncertain significance
(Jul 24, 2019)

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	1	1	not provided	not provided	not provided	clinical testing

Citations

PubMed

A systematic approach to assessing the clinical significance of genetic variants.

Duzkale H, Shen J, McLaughlin H, Alfares A, Kelly MA, Pugh TJ, Funke BH, Rehm HL, Lebo MS.

Clin Genet. 2013 Nov;84(5):453-63. doi: 10.1111/cge.12257.

PubMed [citation]

PMID:: 24033266
PMCID:: PMC3995020

Details of each submission

From Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, SCV001365556.1

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

Description

The p.Pro1797Ser variant in PCDH15 has not been previously reported in individuals with hearing loss or Usher syndrome, but has been identified in 0.01% (4/28314) of South Asian chromosomes by gnomAD (http://gnomad.broadinstitute.org). Computational prediction tools and conservation analyses suggest that this variant may not impact the protein, though this information is not predictive enough to rule out pathogenicity. In summary, the clinical significance of this variant is uncertain. ACMG/AMP Criteria applied: PM2_Supporting, BP4.

#	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		1	not provided	1	not provided

Last Updated: Sep 29, 2024

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