NM_015215.4(CAMTA1):c.838del (p.Ser280fs) AND not provided

Germline classification:: Pathogenic/Likely pathogenic (2 submissions)
Last evaluated:: Feb 24, 2018
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:: RCV000480295.6

Allele description [Variation Report for NM_015215.4(CAMTA1):c.838del (p.Ser280fs)]

NM_015215.4(CAMTA1):c.838del (p.Ser280fs)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

1p36.23

Genomic location:

Preferred name:

NM_015215.4(CAMTA1):c.838del (p.Ser280fs)

HGVS:

NC_000001.11:g.7663385del
NG_053148.1:g.883062del
NM_001349608.2:c.748del
NM_001349609.2:c.838del
NM_001349610.2:c.838del
NM_001349612.2:c.748del
NM_015215.4:c.838delMANE SELECT
NP_001336537.1:p.Ser250fs
NP_001336538.1:p.Ser280fs
NP_001336539.1:p.Ser280fs
NP_001336541.1:p.Ser250fs
NP_056030.1:p.Ser280fs
NC_000001.10:g.7723445del
NC_000001.10:g.7723445delA
NM_015215.3:c.838del
NM_015215.3:c.838delA

Protein change:

S250fs

Links:

OMIM: 611501.0007; dbSNP: rs1064796146

NCBI 1000 Genomes Browser:

rs1064796146

Molecular consequence:

NM_001349608.2:c.748del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001349609.2:c.838del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001349610.2:c.838del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001349612.2:c.748del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_015215.4:c.838del - frameshift variant - [Sequence Ontology: SO:0001589]

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
SCV000572609	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Likely pathogenic (Jan 18, 2017)	germline	clinical testing	Citation Link,
SCV001581798	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Feb 24, 2018)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 22693284, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000572609

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Likely pathogenic
(Jan 18, 2017)

germline

clinical testing

Citation Link,

SCV001581798

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Feb 24, 2018)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

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
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Intragenic CAMTA1 rearrangements cause non-progressive congenital ataxia with or without intellectual disability.

Thevenon J, Lopez E, Keren B, Heron D, Mignot C, Altuzarra C, Béri-Dexheimer M, Bonnet C, Magnin E, Burglen L, Minot D, Vigneron J, Morle S, Anheim M, Charles P, Brice A, Gallagher L, Amiel J, Haffen E, Mach C, Depienne C, Doummar D, et al.

J Med Genet. 2012 Jun;49(6):400-8. doi: 10.1136/jmedgenet-2012-100856.

PubMed [citation]

PMID:: 22693284

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 GeneDx, SCV000572609.3

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

Description

The c.838delA variant in the CAMTA1 gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. The c.838delA variant causes a frameshift starting with codon Serine 280, changes this amino acid to an Alanine residue, and creates a premature Stop codon at position 110 of the new reading frame, denoted p.Ser280AlafsX110. This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The c.838delA variant was not observed in approximately 6500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. We interpret c.838delA as a likely pathogenic variant.

#	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 Labcorp Genetics (formerly Invitae), Labcorp, SCV001581798.4

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

Description

This sequence change creates a premature translational stop signal (p.Ser280Alafs*110) in the CAMTA1 gene. It is expected to result in an absent or disrupted protein product. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with CAMTA1-related disease. ClinVar contains an entry for this variant (Variation ID: 422992). Loss-of-function variants in CAMTA1 are known to be pathogenic (PMID: 22693284). For these reasons, this variant has been classified as Pathogenic.

#	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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