NM_015215.4(CAMTA1):c.946A>G (p.Ser316Gly) AND not provided

Germline classification:: Uncertain significance (3 submissions)
Last evaluated:: Nov 7, 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:: RCV002756915.14

Allele description [Variation Report for NM_015215.4(CAMTA1):c.946A>G (p.Ser316Gly)]

NM_015215.4(CAMTA1):c.946A>G (p.Ser316Gly)

Gene:

CAMTA1:calmodulin binding transcription activator 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1p36.23

Genomic location:

Preferred name:

NM_015215.4(CAMTA1):c.946A>G (p.Ser316Gly)

HGVS:

NC_000001.11:g.7663493A>G
NG_053148.1:g.883170A>G
NG_089151.1:g.385A>G
NM_001349608.2:c.856A>G
NM_001349609.2:c.946A>G
NM_001349610.2:c.946A>G
NM_001349612.2:c.856A>G
NM_001410737.1:c.946A>G
NM_001410738.1:c.874A>G
NM_015215.4:c.946A>GMANE SELECT
NP_001336537.1:p.Ser286Gly
NP_001336538.1:p.Ser316Gly
NP_001336539.1:p.Ser316Gly
NP_001336541.1:p.Ser286Gly
NP_001397666.1:p.Ser316Gly
NP_001397667.1:p.Ser292Gly
NP_056030.1:p.Ser316Gly
NC_000001.10:g.7723553A>G

Protein change:

S286G

Molecular consequence:

NM_001349608.2:c.856A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001349609.2:c.946A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001349610.2:c.946A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001349612.2:c.856A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001410737.1:c.946A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001410738.1:c.874A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_015215.4:c.946A>G - 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
SCV003026401	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Nov 7, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004128092	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Uncertain significance (Mar 1, 2023)	germline	clinical testing	Citation Link,
SCV005197380	Clinical Genetics Laboratory, Skane University Hospital Lund	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Feb 20, 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

SCV003026401

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Nov 7, 2023)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

SCV004128092

CeGaT Center for Human Genetics Tuebingen

criteria provided, single submitter

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

Uncertain significance
(Mar 1, 2023)

germline

clinical testing

Citation Link,

SCV005197380

Clinical Genetics Laboratory, Skane University Hospital Lund

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Feb 20, 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
not provided	germline	yes	2	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

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 Labcorp Genetics (formerly Invitae), Labcorp, SCV003026401.2

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

Description

This sequence change replaces serine, which is neutral and polar, with glycine, which is neutral and non-polar, at codon 316 of the CAMTA1 protein (p.Ser316Gly). This variant is present in population databases (rs752011665, gnomAD 0.02%). This variant has not been reported in the literature in individuals affected with CAMTA1-related conditions. ClinVar contains an entry for this variant (Variation ID: 1984836). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Not Available"; PolyPhen-2: "Benign"; Align-GVGD: "Not Available". The glycine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. 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.

#	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, SCV004128092.10

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

Description

CAMTA1: PP2, BP4

#	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		2	not provided	not provided	not provided

From Clinical Genetics Laboratory, Skane University Hospital Lund, SCV005197380.1

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

#	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: Oct 20, 2024

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