NM_001077415.3(CRELD1):c.234G>T (p.Glu78Asp) AND Atrioventricular septal defect, susceptibility to, 2

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jun 19, 2023
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:: RCV003608354.2

Allele description [Variation Report for NM_001077415.3(CRELD1):c.234G>T (p.Glu78Asp)]

NM_001077415.3(CRELD1):c.234G>T (p.Glu78Asp)

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.234G>T (p.Glu78Asp)

HGVS:

NC_000003.12:g.9934894G>T
NG_017069.1:g.6054G>T
NG_017069.2:g.6062G>T
NG_029376.2:g.22797G>T
NM_001031717.4:c.234G>T
NM_001077415.3:c.234G>TMANE SELECT
NM_001374316.1:c.234G>T
NM_001374317.1:c.234G>T
NM_001374318.1:c.234G>T
NM_001374319.1:c.234G>T
NM_001374320.1:c.234G>T
NM_001410713.1:c.234G>T
NM_015513.6:c.234G>T
NP_001026887.2:p.Glu78Asp
NP_001070883.2:p.Glu78Asp
NP_001361245.1:p.Glu78Asp
NP_001361246.1:p.Glu78Asp
NP_001361247.1:p.Glu78Asp
NP_001361248.1:p.Glu78Asp
NP_001361249.1:p.Glu78Asp
NP_001397642.1:p.Glu78Asp
NP_056328.3:p.Glu78Asp
LRG_1311:g.22797G>T
NC_000003.11:g.9976578G>T
NR_164475.1:n.272G>T
NR_164476.1:n.340G>T
NR_164477.1:n.622G>T

Protein change:

E78D

Molecular consequence:

NM_001031717.4:c.234G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001077415.3:c.234G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001374316.1:c.234G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001374317.1:c.234G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001374318.1:c.234G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001374319.1:c.234G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001374320.1:c.234G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001410713.1:c.234G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_015513.6:c.234G>T - missense variant - [Sequence Ontology: SO:0001583]
NR_164475.1:n.272G>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_164476.1:n.340G>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_164477.1:n.622G>T - 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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Pde8a phosphodiesterase 8A [Mus musculus]
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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004459887	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jun 19, 2023)	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

SCV004459887

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jun 19, 2023)

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	unknown	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

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004459887.1

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

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. This variant has not been reported in the literature in individuals affected with CRELD1-related conditions. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This sequence change replaces glutamic acid, which is acidic and polar, with aspartic acid, which is acidic and polar, at codon 78 of the CRELD1 protein (p.Glu78Asp).

#	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

Last Updated: Sep 29, 2024

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