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NM_006009.4(TUBA1A):c.889G>A (p.Glu297Lys) AND Lissencephaly due to TUBA1A mutation

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
May 26, 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:
RCV002471983.2

Allele description [Variation Report for NM_006009.4(TUBA1A):c.889G>A (p.Glu297Lys)]

NM_006009.4(TUBA1A):c.889G>A (p.Glu297Lys)

Gene:
TUBA1A:tubulin alpha 1a [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
12q13.12
Genomic location:
Preferred name:
NM_006009.4(TUBA1A):c.889G>A (p.Glu297Lys)
HGVS:
  • NC_000012.12:g.49185477C>T
  • NG_008966.1:g.8602G>A
  • NG_125622.1:g.284C>T
  • NM_001270399.2:c.889G>A
  • NM_001270400.2:c.784G>A
  • NM_006009.4:c.889G>AMANE SELECT
  • NP_001257328.1:p.Glu297Lys
  • NP_001257329.1:p.Glu262Lys
  • NP_006000.2:p.Glu297Lys
  • NC_000012.11:g.49579260C>T
  • NM_006009.3:c.889G>A
Protein change:
E262K
Molecular consequence:
  • NM_001270399.2:c.889G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001270400.2:c.784G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_006009.4:c.889G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Lissencephaly due to TUBA1A mutation (LIS3)
Synonyms:
Lissencephaly 3
Identifiers:
MONDO: MONDO:0012703; MedGen: C4305153; Orphanet: 171680; OMIM: 611603

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002767688Victorian Clinical Genetics Services, Murdoch Childrens Research Institute

See additional submitters

criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significance
(May 26, 2020) 		germlineclinical testing

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

Help

Summary from all submissions

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

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From Victorian Clinical Genetics Services, Murdoch Childrens Research Institute, SCV002767688.1

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

Description

Based on the classification scheme VCGS_Germline_v1.1.1, this variant is classified as VUS – 3A. Following criteria are met: 0102 - Loss-of-function is a known mechanism of disease for this gene. (N) 0104 - Dominant Negative is a mechanism of disease for this gene. (N) 0107 - This gene is known to be associated with autosomal dominant disease. (N) 0200 - Variant is predicted to result in a missense amino acid change from glutamic acid to lysine (exon 4). (N) 0251 - Variant is heterozygous. (N) 0301 - Variant is absent from gnomAD. (P) 0501 - Missense variant consistently predicted to be damaging by multiple in silico tools or highly conserved with a major amino acid change. (P) 0603 - Missense variant in a region that is highly intolerant to missense variation (high constraint region). (P) 0705 - No comparable variants have previous evidence for pathogenicity. (N) 0807 - Variant has not previously been reported in a clinical context. (N) 0905 - No segregation evidence has been identified for this variant. (N) 1007 - No published functional evidence has been identified for this variant. (N) 1208 - Inheritance information for this variant is not currently available. (N) Legend: (P) - Pathogenic, (N) - Neutral, (B) - Benign

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

Last Updated: Jun 23, 2024