NM_001384140.1(PCDH15):c.2435T>C (p.Ile812Thr) AND not provided

Germline classification:: Benign/Likely benign (8 submissions)
Last evaluated:: May 1, 2024
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:: RCV000513885.26

Allele description [Variation Report for NM_001384140.1(PCDH15):c.2435T>C (p.Ile812Thr)]

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

Gene:

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

Variant type:

single nucleotide variant

Cytogenetic location:

10q21.1

Genomic location:

Preferred name:

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

HGVS:

NC_000010.11:g.54022983A>G
NG_009191.3:g.1611200T>C
NM_001142763.2:c.2450T>C
NM_001142764.2:c.2435T>C
NM_001142765.2:c.2222T>C
NM_001142766.2:c.2435T>C
NM_001142767.2:c.2324T>C
NM_001142768.2:c.2369T>C
NM_001142769.3:c.2471T>C
NM_001142770.3:c.2435T>C
NM_001142771.2:c.2450T>C
NM_001142772.2:c.2435T>C
NM_001142773.2:c.2369T>C
NM_001354404.2:c.2369T>C
NM_001354411.2:c.2456T>C
NM_001354420.2:c.2435T>C
NM_001354429.2:c.2435T>C
NM_001354430.2:c.2435T>C
NM_001384140.1:c.2435T>CMANE SELECT
NM_033056.4:c.2435T>C
NP_001136235.1:p.Ile817Thr
NP_001136236.1:p.Ile812Thr
NP_001136237.1:p.Ile741Thr
NP_001136238.1:p.Ile812Thr
NP_001136239.1:p.Ile775Thr
NP_001136240.1:p.Ile790Thr
NP_001136241.1:p.Ile824Thr
NP_001136242.1:p.Ile812Thr
NP_001136243.1:p.Ile817Thr
NP_001136244.1:p.Ile812Thr
NP_001136245.1:p.Ile790Thr
NP_001341333.1:p.Ile790Thr
NP_001341340.1:p.Ile819Thr
NP_001341349.1:p.Ile812Thr
NP_001341358.1:p.Ile812Thr
NP_001341359.1:p.Ile812Thr
NP_001371069.1:p.Ile812Thr
NP_149045.3:p.Ile812Thr
NC_000010.10:g.55782743A>G
NM_033056.3:c.2435T>C

Protein change:

I741T

Links:

dbSNP: rs61731363

NCBI 1000 Genomes Browser:

rs61731363

Molecular consequence:

NM_001142763.2:c.2450T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001142764.2:c.2435T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001142765.2:c.2222T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001142766.2:c.2435T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001142767.2:c.2324T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001142768.2:c.2369T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001142769.3:c.2471T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001142770.3:c.2435T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001142771.2:c.2450T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001142772.2:c.2435T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001142773.2:c.2369T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001354404.2:c.2369T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001354411.2:c.2456T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001354420.2:c.2435T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001354429.2:c.2435T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001354430.2:c.2435T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001384140.1:c.2435T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_033056.4:c.2435T>C - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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arylacetamide deacetylase-like 2 isoform X1 [Rattus norvegicus]
arylacetamide deacetylase-like 2 isoform X1 [Rattus norvegicus]
gi|672042477|ref|XP_578020.5|

Protein
Salix purpurea cultivar:00-01-009
Salix purpurea cultivar:00-01-009
Salix purpurea 00-01-009 Bisulfite Sequencing - 00-01-009 epigenomics

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000610806	Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely benign (Apr 11, 2017)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV000885888	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	criteria provided, single submitter (ARUP Molecular Germline Variant Investigation Process 2024)	Benign (Oct 14, 2023)	germline	clinical testing	Citation Link,
SCV001109075	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Benign (Jan 30, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001803026	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Likely benign (Apr 17, 2021)	germline	clinical testing	Citation Link,
SCV001978985	Clinical Genetics, Academic Medical Center - VKGL Data-share Consensus See additional submitters Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	no assertion criteria provided	Likely benign	germline	clinical testing
SCV001979962	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus See additional submitters Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	no assertion criteria provided	Likely benign	germline	clinical testing
SCV005051408	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Likely benign (May 1, 2024)	germline	clinical testing	Citation Link,
SCV005220770	Breakthrough Genomics, Breakthrough Genomics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely benign	germline	not provided	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	yes	1	not provided	not provided	not provided	not provided	clinical testing, not provided
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	not provided	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. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics, SCV000610806.1

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

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	not provided	not provided	not provided	not provided		not provided	0.001386	not provided	not provided

From ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories, SCV000885888.2

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

#	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

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001109075.6

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

#	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

From GeneDx, SCV001803026.1

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

Description

This variant is associated with the following publications: (PMID: 27766948)

#	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 Clinical Genetics, Academic Medical Center - VKGL Data-share Consensus, SCV001978985.1

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

#	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 Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus, SCV001979962.1

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

#	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 CeGaT Center for Human Genetics Tuebingen, SCV005051408.4

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

Description

PCDH15: BS1

#	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		1	not provided	not provided	not provided

From Breakthrough Genomics, Breakthrough Genomics, SCV005220770.1

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

#	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

Last Updated: Oct 8, 2024

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