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NM_006888.6(CALM1):c.88A>C (p.Thr30Pro) AND not provided

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Mar 2, 2016
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:
RCV000431318.1

Allele description [Variation Report for NM_006888.6(CALM1):c.88A>C (p.Thr30Pro)]

NM_006888.6(CALM1):c.88A>C (p.Thr30Pro)

Gene:
CALM1:calmodulin 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
14q32.11
Genomic location:
Preferred name:
NM_006888.6(CALM1):c.88A>C (p.Thr30Pro)
HGVS:
  • NC_000014.9:g.90401312A>C
  • NG_013338.1:g.9330A>C
  • NM_001363669.2:c.-21A>C
  • NM_001363670.2:c.91A>C
  • NM_006888.6:c.88A>CMANE SELECT
  • NP_001350599.1:p.Thr31Pro
  • NP_008819.1:p.Thr30Pro
  • NC_000014.8:g.90867656A>C
  • NM_006888.4:c.88A>C
Protein change:
T30P
Links:
dbSNP: rs1057521851
NCBI 1000 Genomes Browser:
rs1057521851
Molecular consequence:
  • NM_001363669.2:c.-21A>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001363670.2:c.91A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_006888.6:c.88A>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: CN517202

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000524774GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Likely pathogenic
(Mar 2, 2016) 		germlineclinical testing

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From GeneDx, SCV000524774.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The T30P variant in the CALM1 gene has not been reported previously as a pathogenic variant, nor as a benign variant, to our knowledge. The T30P variant was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. The T30P variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. This substitution occurs at a position that is conserved across species. However, in silico analysis is inconsistent in its predictions as to whether or not the variant is damaging to the protein structure/function. The T30P variant is a strong candidate for a pathogenic variant, however, the possibility it may be a rare benign variant cannot be excluded.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Apr 23, 2022