VCV000160150.7 - ClinVar

NM_006009.4(TUBA1A):c.162T>A (p.Ser54Arg)

Germline

Classification

The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.

(2)

Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.

Likely pathogenic

criteria provided, multiple submitters, no conflicts

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_006009.4(TUBA1A):c.162T>A (p.Ser54Arg)

Variation ID: 160150 Accession: VCV000160150.7

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 12q13.12 12: 49186675 (GRCh38) [ NCBI UCSC ] 12: 49580458 (GRCh37) [ NCBI UCSC ]

Timeline in ClinVar

	First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.	Last submission Help The date of the most recent submission for each type of classification for this variant.	Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline	Nov 23, 2014	Apr 21, 2019	Jul 1, 2018

HGVS

Nucleotide	Protein	Molecular consequence
NM_006009.4:c.162T>A MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_006000.2:p.Ser54Arg	missense
NM_001270399.2:c.162T>A	NP_001257328.1:p.Ser54Arg	missense
NM_001270400.2:c.57T>A	NP_001257329.1:p.Ser19Arg	missense
NC_000012.12:g.49186675A>T
NC_000012.11:g.49580458A>T
NG_008966.1:g.7404T>A

... more HGVS ... less HGVS

Protein change

S54R, S19R

Other names

Canonical SPDI

NC_000012.12:49186674:A:T

Functional consequence Help The effect of the variant on RNA or protein function, based on experimental evidence from submitters.

Global minor allele frequency (GMAF) Help The global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.

Allele frequency Help The frequency of the allele represented by this VCV record.

Links

ClinGen: CA213264 dbSNP: rs587784486 VarSome

Genes

Gene	OMIM	ClinGen Gene Dosage Sensitivity Curation		Variation Viewer Help Links to Variation Viewer, a genome browser to view variation data from NCBI databases.	Related variants
Gene	OMIM	HI score Help The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.	TS score Help The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.		Within gene Help The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants.	All Help The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene.
TUBA1A		No evidence available	No evidence available	GRCh38 GRCh37	370	381

Conditions - Germline

Condition Help The condition for this variant-condition (RCV) record in ClinVar.	Classification Help The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions)	Review status Help The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status.	Last evaluated Help The most recent date that a submitter evaluated this variant for the condition.	Variation/condition record Help The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page.
Lissencephaly due to TUBA1A mutation	Likely pathogenic (1)	criteria provided, single submitter	Jun 28, 2013	RCV000147802.6
Tubulinopathy	Likely pathogenic (1)	criteria provided, single submitter	Jul 1, 2018	RCV000767515.3

Submissions - Germline

Classification Help The submitted germline classification for each SCV record. (Last evaluated)	Review status Help Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria)	Condition Help The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant.	Submitter Help The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar.	More information Help This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.
Likely pathogenic (Jun 28, 2013)	criteria provided, single submitter (ACMG Guidelines, 2007) Method: clinical testing	Lissencephaly 3 (Autosomal dominant inheritance) Affected status: yes Allele origin: germline	Genetic Services Laboratory, University of Chicago Accession: SCV000195275.1 First in ClinVar: Nov 23, 2014 Last updated: Nov 23, 2014
Likely pathogenic (Jul 01, 2018)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: literature only	Tubulinopathies Affected status: yes Allele origin: germline	Institute of Human Genetics, FAU Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg Accession: SCV000898130.1 First in ClinVar: Apr 21, 2019 Last updated: Apr 21, 2019	Publications: PubMed (1) PubMed: 30744660 DOI: 10.1101/427948 DOI: 10.1101/427948 Comment: A variant that is classified as likely pathogenic has been identified in the TUBA1A gene in a born individual of unknown sex. The c.162T>A, p.(Ser54Arg) … (more) A variant that is classified as likely pathogenic has been identified in the TUBA1A gene in a born individual of unknown sex. The c.162T>A, p.(Ser54Arg) variant has been reported as a variant of germline/unknown origin. (less) Number of individuals with the variant: 1

Germline Functional Evidence

There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for germline classification of this variant

Title	Author	Journal	Year	Link
The mutational and phenotypic spectrum of TUBA1A-associated tubulinopathy.	Hebebrand M	Orphanet journal of rare diseases	2019	PMID: 30744660

Text-mined citations for rs587784486 ...

These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Jun 23, 2024

ClinVar Genomic variation as it relates to human health

NM_006009.4(TUBA1A):c.162T>A (p.Ser54Arg)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for rs587784486 ...