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NM_001378615.1(CC2D2A):c.1691C>T (p.Thr564Met) AND Inborn genetic diseases

Germline classification:
Likely benign (1 submission)
Last evaluated:
Jan 27, 2022
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:
RCV002518166.2

Allele description [Variation Report for NM_001378615.1(CC2D2A):c.1691C>T (p.Thr564Met)]

NM_001378615.1(CC2D2A):c.1691C>T (p.Thr564Met)

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.1691C>T (p.Thr564Met)
HGVS:
  • NC_000004.12:g.15537003C>T
  • NG_013035.1:g.72138C>T
  • NM_001080522.2:c.1691C>T
  • NM_001378615.1:c.1691C>TMANE SELECT
  • NM_001378617.1:c.1544C>T
  • NP_001073991.2:p.Thr564Met
  • NP_001365544.1:p.Thr564Met
  • NP_001365546.1:p.Thr515Met
  • LRG_697t1:c.1691C>T
  • LRG_697:g.72138C>T
  • LRG_697p1:p.Thr564Met
  • NC_000004.11:g.15538626C>T
Protein change:
T515M
Links:
dbSNP: rs201954181
NCBI 1000 Genomes Browser:
rs201954181
Molecular consequence:
  • NM_001080522.2:c.1691C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001378615.1:c.1691C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001378617.1:c.1544C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Inborn genetic diseases
Identifiers:
MeSH: D030342; MedGen: C0950123

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003744671Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Likely benign
(Jan 27, 2022) 		germlineclinical testing

Citation Link

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Summary from all submissions

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

Details of each submission

From Ambry Genetics, SCV003744671.2

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

Description

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

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

Last Updated: Nov 3, 2024