NM_020461.4(TUBGCP6):c.3090_3091del (p.Gly1032fs) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Dec 30, 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:: RCV001384129.7

Allele description [Variation Report for NM_020461.4(TUBGCP6):c.3090_3091del (p.Gly1032fs)]

NM_020461.4(TUBGCP6):c.3090_3091del (p.Gly1032fs)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

22q13.33

Genomic location:

Preferred name:

NM_020461.4(TUBGCP6):c.3090_3091del (p.Gly1032fs)

HGVS:

NC_000022.11:g.50221268_50221269del
NG_032160.1:g.28703_28704del
NM_020461.4:c.3090_3091delMANE SELECT
NP_065194.3:p.Gly1032fs
NC_000022.10:g.50659697_50659698del

Protein change:

G1032fs

Links:

dbSNP: rs1491234697

NCBI 1000 Genomes Browser:

rs1491234697

Molecular consequence:

NM_020461.4:c.3090_3091del - frameshift variant - [Sequence Ontology: SO:0001589]

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
SCV001583514	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Dec 30, 2022)	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

SCV001583514

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Dec 30, 2022)

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, SCV001583514.5

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

Description

For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 1071616). This variant has not been reported in the literature in individuals affected with TUBGCP6-related conditions. This variant is present in population databases (rs796321813, gnomAD 0.007%). This sequence change creates a premature translational stop signal (p.Gly1032Trpfs*10) 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).

#	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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