NM_001077415.3(CRELD1):c.565G>A (p.Gly189Ser) AND Atrioventricular septal defect, susceptibility to, 2

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jan 14, 2022
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:: RCV002272798.2

Allele description [Variation Report for NM_001077415.3(CRELD1):c.565G>A (p.Gly189Ser)]

NM_001077415.3(CRELD1):c.565G>A (p.Gly189Ser)

Gene:

CRELD1:cysteine rich with EGF like domains 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

3p25.3

Genomic location:

Preferred name:

NM_001077415.3(CRELD1):c.565G>A (p.Gly189Ser)

HGVS:

NC_000003.12:g.9940954G>A
NG_017069.1:g.12114G>A
NM_001031717.4:c.565G>A
NM_001077415.3:c.565G>AMANE SELECT
NM_001374316.1:c.565G>A
NM_001374317.1:c.565G>A
NM_001374318.1:c.565G>A
NM_001374319.1:c.565G>A
NM_001374320.1:c.565G>A
NM_015513.6:c.565G>A
NP_001026887.2:p.Gly189Ser
NP_001070883.2:p.Gly189Ser
NP_001361245.1:p.Gly189Ser
NP_001361246.1:p.Gly189Ser
NP_001361247.1:p.Gly189Ser
NP_001361248.1:p.Gly189Ser
NP_001361249.1:p.Gly189Ser
NP_056328.3:p.Gly189Ser
NC_000003.11:g.9982638G>A
NR_164475.1:n.603G>A
NR_164476.1:n.579G>A
NR_164477.1:n.953G>A

Protein change:

G189S

Links:

dbSNP: rs2124849361

NCBI 1000 Genomes Browser:

rs2124849361

Molecular consequence:

NM_001031717.4:c.565G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001077415.3:c.565G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001374316.1:c.565G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001374317.1:c.565G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001374318.1:c.565G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001374319.1:c.565G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001374320.1:c.565G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_015513.6:c.565G>A - missense variant - [Sequence Ontology: SO:0001583]
NR_164475.1:n.603G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_164476.1:n.579G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_164477.1:n.953G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Atrioventricular septal defect, susceptibility to, 2
Synonyms:: Atrioventricular septal defect 2
Identifiers:: MONDO: MONDO:0011650; MedGen: C1853508; OMIM: 606217

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002557018	Genetics and Molecular Pathology, SA Pathology See additional submitters Shariant Australia, Australian Genomics	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Jan 14, 2022)	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

SCV002557018

Genetics and Molecular Pathology, SA Pathology

See additional submitters

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Jan 14, 2022)

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

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 Genetics and Molecular Pathology, SA Pathology, SCV002557018.2

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

Description

The CRELD1 c.565G>A variant is classified as a VARIANT of UNCERTAIN SIGNIFICANCE (PP3, PM2) The CRELD1 c.565G>A variant is a single nucleotide change in exon 6/11 of the CRELD1 gene, which is predicted to change the amino acid glycine at position 189 in the protein to serine. This variant has not been reported in dbSNP and is absent from population databases (PM2). This variant has not been reported in the ClinVar or HGMD disease databases. Computational predictions support a deleterious effect on the gene or gene product (PP3).

#	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: Dec 24, 2023

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