NM_001378615.1(CC2D2A):c.3046G>A (p.Glu1016Lys) AND not provided

Germline classification:: Uncertain significance (3 submissions)
Last evaluated:: Dec 1, 2023
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:: RCV000344416.22

Allele description [Variation Report for NM_001378615.1(CC2D2A):c.3046G>A (p.Glu1016Lys)]

NM_001378615.1(CC2D2A):c.3046G>A (p.Glu1016Lys)

Gene:

CC2D2A:coiled-coil and C2 domain containing 2A [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

4p15.32

Genomic location:

Preferred name:

NM_001378615.1(CC2D2A):c.3046G>A (p.Glu1016Lys)

HGVS:

NC_000004.12:g.15563386G>A
NG_013035.1:g.98521G>A
NM_001080522.2:c.3046G>A
NM_001378615.1:c.3046G>AMANE SELECT
NM_001378617.1:c.2899G>A
NP_001073991.2:p.Glu1016Lys
NP_001365544.1:p.Glu1016Lys
NP_001365546.1:p.Glu967Lys
LRG_697t1:c.3046G>A
LRG_697:g.98521G>A
LRG_697p1:p.Glu1016Lys
NC_000004.11:g.15565009G>A

Protein change:

E1016K

Links:

dbSNP: rs373960465

NCBI 1000 Genomes Browser:

rs373960465

Molecular consequence:

NM_001080522.2:c.3046G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001378615.1:c.3046G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001378617.1:c.2899G>A - missense variant - [Sequence Ontology: SO:0001583]

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
SCV000345696	Eurofins Ntd Llc (ga)	criteria provided, single submitter (EGL ClinVar v180209 classification definitions)	Uncertain significance (Feb 22, 2018)	germline	clinical testing	Citation Link,
SCV002013806	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Uncertain significance (Aug 13, 2021)	germline	clinical testing	Citation Link,
SCV004701195	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Uncertain significance (Dec 1, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000345696

Eurofins Ntd Llc (ga)

criteria provided, single submitter

(EGL ClinVar v180209 classification definitions)

Uncertain significance
(Feb 22, 2018)

germline

clinical testing

Citation Link,

SCV002013806

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Uncertain significance
(Aug 13, 2021)

germline

clinical testing

Citation Link,

SCV004701195

CeGaT Center for Human Genetics Tuebingen

criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)

Uncertain significance
(Dec 1, 2023)

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	unknown	2	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	yes	1	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From Eurofins Ntd Llc (ga), SCV000345696.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	2	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		2	not provided	not provided	not provided

From GeneDx, SCV002013806.2

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

Description

In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge

#	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, SCV004701195.12

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

Last Updated: May 25, 2025

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