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NM_001003800.2(BICD2):c.2108C>T (p.Thr703Met) AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Apr 5, 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:
RCV000345846.1

Allele description [Variation Report for NM_001003800.2(BICD2):c.2108C>T (p.Thr703Met)]

NM_001003800.2(BICD2):c.2108C>T (p.Thr703Met)

Gene:
BICD2:BICD cargo adaptor 2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
9q22.31
Genomic location:
Preferred name:
NM_001003800.2(BICD2):c.2108C>T (p.Thr703Met)
HGVS:
  • NC_000009.12:g.92717947G>A
  • NG_033908.1:g.51855C>T
  • NM_001003800.2:c.2108C>TMANE SELECT
  • NM_015250.4:c.2108C>T
  • NP_001003800.1:p.Thr703Met
  • NP_056065.1:p.Thr703Met
  • NC_000009.11:g.95480229G>A
  • NM_001003800.1:c.2108C>T
  • NM_015250.3:c.2108C>T
  • Q8TD16:p.Thr703Met
Protein change:
T703M; THR703MET
Links:
UniProtKB: Q8TD16#VAR_070117; OMIM: 609797.0002; dbSNP: rs371707778
NCBI 1000 Genomes Browser:
rs371707778
Molecular consequence:
  • NM_001003800.2:c.2108C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_015250.4:c.2108C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000329948GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))
Pathogenic
(Apr 5, 2016)
germlineclinical testing

Citation Link

Summary from all submissions

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

Details of each submission

From GeneDx, SCV000329948.5

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

Description

The maternally inherited T703M pathogenic variant in the BICD2 gene has been reported previously as aheterozygous pathogenic variant in a father and son with spinal muscular atrophy (Neveling et al., 2013). Usingimmunoblot analysis, fibroblasts from the affected patients had reduced BICD2 levels compared to control fibroblastsand using immunostaining, the fibroblasts from the affected patients showed strong Golgi fragmentation and BICD2trapped in the Golgi (Neveling et al., 2013). The T703M variant was not observed with any significant frequency inapproximately 6500 individuals of European and African American ancestry in the NHLBI Exome SequencingProject, indicating it is not a common benign variant in these populations. The T703M variant is a non-conservativeamino 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 in the 3rd coiled-coil domain at a position that isconserved across species. In silico analysis predicts this variant is probably damaging to the proteinstructure/function. We interpret T703M as a pathogenic variant.

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

Last Updated: Sep 29, 2024