NM_006363.6(SEC23B):c.1512T>C (p.Asn504=) AND not provided

Germline classification:: Conflicting interpretations of pathogenicity (5 submissions)
Last evaluated:: Mar 1, 2024
Review status:: criteria provided, conflicting classifications

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:: RCV001509053.26

Allele description [Variation Report for NM_006363.6(SEC23B):c.1512T>C (p.Asn504=)]

NM_006363.6(SEC23B):c.1512T>C (p.Asn504=)

Gene:

SEC23B:SEC23 homolog B, COPII coat complex component [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

20p11.23

Genomic location:

Preferred name:

NM_006363.6(SEC23B):c.1512T>C (p.Asn504=)

HGVS:

NC_000020.11:g.18543019T>C
NG_016281.2:g.40538T>C
NM_001172745.3:c.1512T>C
NM_001172746.3:c.1458T>C
NM_006363.6:c.1512T>CMANE SELECT
NM_032985.6:c.1512T>C
NM_032986.5:c.1512T>C
NP_001166216.1:p.Asn504=
NP_001166217.1:p.Asn486=
NP_006354.2:p.Asn504=
NP_116780.1:p.Asn504=
NP_116781.1:p.Asn504=
LRG_1134t1:c.1512T>C
LRG_1134:g.40538T>C
LRG_1134p1:p.Asn504=
NC_000020.10:g.18523663T>C
NM_001172745.2:c.1512T>C
NM_006363.4:c.1512T>C
p.Asn504=

Links:

dbSNP: rs138198461

NCBI 1000 Genomes Browser:

rs138198461

Molecular consequence:

NM_001172745.3:c.1512T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001172746.3:c.1458T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_006363.6:c.1512T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_032985.6:c.1512T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_032986.5:c.1512T>C - synonymous variant - [Sequence Ontology: SO:0001819]

Observations:

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
SCV001715555	Mayo Clinic Laboratories, Mayo Clinic	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Jan 26, 2023)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 26522472, 25741868
SCV001977905	Genome Diagnostics Laboratory, University Medical Center Utrecht - 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
SCV001980526	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
SCV002048312	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	criteria provided, single submitter (ARUP Molecular Germline Variant Investigation Process 2024)	Likely benign (Jun 15, 2023)	germline	clinical testing	Citation Link,
SCV002821062	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Likely benign (Mar 1, 2024)	germline	clinical testing	Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	19	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	31	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Germline Heterozygous Variants in SEC23B Are Associated with Cowden Syndrome and Enriched in Apparently Sporadic Thyroid Cancer.

Yehia L, Niazi F, Ni Y, Ngeow J, Sankunny M, Liu Z, Wei W, Mester JL, Keri RA, Zhang B, Eng C.

Am J Hum Genet. 2015 Nov 5;97(5):661-76. doi: 10.1016/j.ajhg.2015.10.001. Epub 2015 Oct 29.

PubMed [citation]

PMID:: 26522472
PMCID:: PMC4667132

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 Mayo Clinic Laboratories, Mayo Clinic, SCV001715555.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	31	not provided	not provided	clinical testing	PubMed (2)

#	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		31	not provided	not provided	not provided

From Genome Diagnostics Laboratory, University Medical Center Utrecht - VKGL Data-share Consensus, SCV001977905.1

#	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, SCV001980526.1

#	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 ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories, SCV002048312.2

#	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 CeGaT Center for Human Genetics Tuebingen, SCV002821062.8

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	19	not provided	not provided	clinical testing	not provided

Description

SEC23B: BP4, BP7

#	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		19	not provided	not provided	not provided

Last Updated: May 1, 2024

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