NM_020461.4(TUBGCP6):c.3082C>T (p.Gln1028Ter) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Oct 19, 2020
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:: RCV001389901.5

Allele description [Variation Report for NM_020461.4(TUBGCP6):c.3082C>T (p.Gln1028Ter)]

NM_020461.4(TUBGCP6):c.3082C>T (p.Gln1028Ter)

Gene:

TUBGCP6:tubulin gamma complex component 6 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

22q13.33

Genomic location:

Preferred name:

NM_020461.4(TUBGCP6):c.3082C>T (p.Gln1028Ter)

HGVS:

NC_000022.11:g.50221277G>A
NG_032160.1:g.28695C>T
NM_020461.4:c.3082C>TMANE SELECT
NP_065194.3:p.Gln1028Ter
NC_000022.10:g.50659706G>A

Protein change:

Q1028*

Links:

dbSNP: rs755344399

NCBI 1000 Genomes Browser:

rs755344399

Molecular consequence:

NM_020461.4:c.3082C>T - nonsense - [Sequence Ontology: SO:0001587]

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
SCV001591424	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Oct 19, 2020)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 25344692, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001591424

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Oct 19, 2020)

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

Citations

PubMed

Mutations in PLK4, encoding a master regulator of centriole biogenesis, cause microcephaly, growth failure and retinopathy.

Martin CA, Ahmad I, Klingseisen A, Hussain MS, Bicknell LS, Leitch A, Nürnberg G, Toliat MR, Murray JE, Hunt D, Khan F, Ali Z, Tinschert S, Ding J, Keith C, Harley ME, Heyn P, Müller R, Hoffmann I, Cormier-Daire V, Dollfus H, Dupuis L, et al.

Nat Genet. 2014 Dec;46(12):1283-1292. doi: 10.1038/ng.3122. Epub 2014 Oct 26.

PubMed [citation]

PMID:: 25344692
PMCID:: PMC4676084

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 Labcorp Genetics (formerly Invitae), Labcorp, SCV001591424.4

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

Description

Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site, but this prediction has not been confirmed by published transcriptional studies. This variant has not been reported in the literature in individuals with TUBGCP6-related conditions. This variant is present in population databases (rs755344399, ExAC 0.002%). This sequence change creates a premature translational stop signal (p.Gln1028*) in the TUBGCP6 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in TUBGCP6 are known to be pathogenic (PMID: 25344692). 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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