NM_006364.4(SEC23A):c.59G>A (p.Ser20Asn) AND Craniolenticulosutural dysplasia

Germline classification:: Uncertain significance (1 submission)
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:: RCV003388967.2

Allele description [Variation Report for NM_006364.4(SEC23A):c.59G>A (p.Ser20Asn)]

NM_006364.4(SEC23A):c.59G>A (p.Ser20Asn)

Gene:

SEC23A:SEC23 homolog A, COPII coat complex component [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

14q21.1

Genomic location:

Preferred name:

NM_006364.4(SEC23A):c.59G>A (p.Ser20Asn)

HGVS:

NC_000014.9:g.39096060C>T
NG_012157.1:g.12174G>A
NM_006364.4:c.59G>AMANE SELECT
NP_006355.2:p.Ser20Asn
NC_000014.8:g.39565264C>T

Protein change:

S20N

Molecular consequence:

NM_006364.4:c.59G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Craniolenticulosutural dysplasia (CLSD)
Synonyms:: BOYADJIEV-JABS SYNDROME
Identifiers:: MONDO: MONDO:0011911; MedGen: C1843042; Orphanet: 50814; OMIM: 607812

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004100921	Neuberg Centre For Genomic Medicine, NCGM	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance	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

SCV004100921

Neuberg Centre For Genomic Medicine, NCGM

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance

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

Citations

PubMed

Nothing to display

Details of each submission

From Neuberg Centre For Genomic Medicine, NCGM, SCV004100921.1

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

Description

The missense variant p.S20N in SEC23A (NM_006364.4) has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. The p.S20N variant is novel (not in any individuals) in gnomAD Exomes and is novel (not in any individuals) in 1000 Genomes. The p.S20N missense variant is predicted to be damaging by both SIFT and PolyPhen2. The serine residue at codon 20 of SEC23A is conserved in all mammalian species. The nucleotide c.59 in SEC23A is predicted conserved by GERP++ and PhyloP across 100 vertebrates. For these reasons, this variant has been classified as Uncertain Significance. The same variant has been detected in heterozygous state in his spouse.

#	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: Apr 6, 2024

ClinVar

Relating variation to medicine