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NM_001384140.1(PCDH15):c.2435T>C (p.Ile812Thr)

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Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
10 (Most recent: Oct 15, 2021)
Last evaluated:
Apr 17, 2021
Accession:
VCV000178628.11
Variation ID:
178628
Description:
single nucleotide variant
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NM_001384140.1(PCDH15):c.2435T>C (p.Ile812Thr)

Allele ID
174717
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
10q21.1
Genomic location
10: 54022983 (GRCh38) GRCh38 UCSC
10: 55782743 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000010.10:g.55782743A>G
NC_000010.11:g.54022983A>G
NG_009191.3:g.1611200T>C
... more HGVS
Protein change
I812T, I775T, I817T, I824T, I741T, I790T, I819T
Other names
-
Canonical SPDI
NC_000010.11:54022982:A:G
Functional consequence
-
Global minor allele frequency (GMAF)
0.00399 (G)

Allele frequency
Exome Aggregation Consortium (ExAC) 0.00090
1000 Genomes Project 0.00399
The Genome Aggregation Database (gnomAD) 0.00312
The Genome Aggregation Database (gnomAD), exomes 0.00070
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00284
The Genome Aggregation Database (gnomAD) 0.00325
Trans-Omics for Precision Medicine (TOPMed) 0.00356
Trans-Omics for Precision Medicine (TOPMed) 0.00341
Links
ClinGen: CA182695
dbSNP: rs61731363
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign/Likely benign 2 criteria provided, multiple submitters, no conflicts Dec 19, 2014 RCV000155383.3
Benign/Likely benign 6 criteria provided, multiple submitters, no conflicts Apr 17, 2021 RCV000513885.9
Likely benign 1 criteria provided, single submitter Jan 9, 2017 RCV000664808.1
Likely benign 1 criteria provided, single submitter Jan 12, 2018 RCV001104967.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
PCDH15 - - GRCh38
GRCh37
1647 1707

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(May 07, 2012)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine
Accession: SCV000205070.5
Submitted: (Mar 21, 2019)
Evidence details
Comment:
Ile812Thr in Exon 19 of PCDH15: This variant is not expected to have clinical si gnificance because it has been identified in 0.7% (26/3738) of … (more)
Benign
(Dec 19, 2014)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000226971.5
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Likely benign
(Apr 11, 2017)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics
Accession: SCV000610806.1
Submitted: (Oct 05, 2017)
Evidence details
Likely benign
(Jan 09, 2017)
criteria provided, single submitter
Method: clinical testing
Usher syndrome type 1F
Allele origin: unknown
Counsyl
Accession: SCV000788823.1
Submitted: (Jul 10, 2018)
Evidence details
Publications
PubMed (1)
Benign
(Aug 14, 2017)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
Accession: SCV000885888.1
Submitted: (Oct 10, 2018)
Evidence details
Likely benign
(Jan 12, 2018)
criteria provided, single submitter
Method: clinical testing
Usher syndrome type 1
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001261876.1
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more)
Benign
(Dec 05, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001109075.3
Submitted: (Jan 07, 2021)
Evidence details
Likely benign
(Apr 17, 2021)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001803026.1
Submitted: (Aug 20, 2021)
Evidence details
Comment:
This variant is associated with the following publications: (PMID: 27766948)
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: germline
Clinical Genetics,Academic Medical Center
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001978985.1
Submitted: (Oct 15, 2021)
Evidence details
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: germline
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001979962.1
Submitted: (Oct 15, 2021)
Evidence details

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
Utilization of amplicon-based targeted sequencing panel for the massively parallel sequencing of sporadic hearing impairment patients from Saudi Arabia. Dallol A BMC medical genetics 2016 PMID: 27766948
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=PCDH15 - - - -

Text-mined citations for rs61731363...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Nov 27, 2021