NM_020461.4(TUBGCP6):c.589T>C (p.Ser197Pro) AND not provided

Clinical significance:Uncertain significance (Last evaluated: Feb 16, 2021)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
3 submissions [Details]
Record status:
current
Accession:
RCV000997946.6

Allele description [Variation Report for NM_020461.4(TUBGCP6):c.589T>C (p.Ser197Pro)]

NM_020461.4(TUBGCP6):c.589T>C (p.Ser197Pro)

Gene:
TUBGCP6:tubulin gamma complex associated protein 6 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
22q13.33
Genomic location:
Preferred name:
NM_020461.4(TUBGCP6):c.589T>C (p.Ser197Pro)
HGVS:
  • NC_000022.11:g.50243871A>G
  • NG_029758.1:g.12535T>C
  • NG_032160.1:g.6101T>C
  • NM_020461.4:c.589T>CMANE SELECT
  • NP_065194.3:p.Ser197Pro
  • NC_000022.10:g.50682300A>G
  • NM_020461.3:c.589T>C
Protein change:
S197P
Links:
dbSNP: rs138586345
NCBI 1000 Genomes Browser:
rs138586345
Molecular consequence:
  • NM_020461.4:c.589T>C - missense variant - [Sequence Ontology: SO:0001583]
Observations:
1

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001153722CeGaT Praxis fuer Humangenetik Tuebingencriteria provided, single submitter
Uncertain significance
(Dec 1, 2016)
germlineclinical testing

Citation Link,

SCV001232598Invitaecriteria provided, single submitter
Uncertain significance
(Oct 19, 2020)
germlineclinical testing

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

SCV001824027GeneDxcriteria provided, single submitter
Uncertain significance
(Feb 16, 2021)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not providednot providednot providednot providedclinical testing
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical 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):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From CeGaT Praxis fuer Humangenetik Tuebingen, SCV001153722.7

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided1not providednot providednot provided

From Invitae, SCV001232598.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

This sequence change replaces serine with proline at codon 197 of the TUBGCP6 protein (p.Ser197Pro). The serine residue is weakly conserved and there is a moderate physicochemical difference between serine and proline. This variant is present in population databases (rs138586345, ExAC 0.2%). This variant has not been reported in the literature in individuals with TUBGCP6-related disease. Algorithms developed to predict the effect of missense changes on protein structure and function do not agree on the potential impact of this missense change (SIFT: Tolerated; PolyPhen-2: Probably Damaging; Align-GVGD: Class C0). 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.

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

From GeneDx, SCV001824027.1

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

Description

Observed with a nonsense variant on the opposite allele (in trans) in a patient with lissencephaly, generalized tonic clonic seizures, myoclonic seizures, and moderate intellectual disability in the published literature (Kolbjer et al., 2021); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; This variant is associated with the following publications: (PMID: 33453472)

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

Last Updated: Oct 6, 2021

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