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NM_031206.7(LAS1L):c.1282G>A (p.Val428Met) AND Wilson-Turner syndrome

Germline classification:
Uncertain significance (2 submissions)
Last evaluated:
Jul 8, 2020
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV001350405.9

Allele description [Variation Report for NM_031206.7(LAS1L):c.1282G>A (p.Val428Met)]

NM_031206.7(LAS1L):c.1282G>A (p.Val428Met)

Gene:
LAS1L:LAS1 like ribosome biogenesis factor [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Xq12
Genomic location:
Preferred name:
NM_031206.7(LAS1L):c.1282G>A (p.Val428Met)
HGVS:
  • NC_000023.11:g.65524074C>T
  • NG_016369.1:g.15733G>A
  • NM_001170649.2:c.1231G>A
  • NM_001170650.2:c.1105G>A
  • NM_001375328.1:c.1282G>A
  • NM_001375329.1:c.1282G>A
  • NM_001375330.1:c.1282G>A
  • NM_001375331.1:c.1231G>A
  • NM_001375332.1:c.325G>A
  • NM_001375333.1:c.1231G>A
  • NM_001375334.1:c.1282G>A
  • NM_001375335.1:c.1282G>A
  • NM_001375336.1:c.1231G>A
  • NM_001375337.1:c.1231G>A
  • NM_031206.4:c.1282G>A
  • NM_031206.7:c.1282G>AMANE SELECT
  • NP_001164120.1:p.Val411Met
  • NP_001164121.1:p.Val369Met
  • NP_001362257.1:p.Val428Met
  • NP_001362258.1:p.Val428Met
  • NP_001362259.1:p.Val428Met
  • NP_001362260.1:p.Val411Met
  • NP_001362261.1:p.Val109Met
  • NP_001362262.1:p.Val411Met
  • NP_001362263.1:p.Val428Met
  • NP_001362264.1:p.Val428Met
  • NP_001362265.1:p.Val411Met
  • NP_001362266.1:p.Val411Met
  • NP_112483.1:p.Val428Met
  • NC_000023.10:g.64743954C>T
  • NR_164681.1:n.1354G>A
Protein change:
V109M
Links:
dbSNP: rs1190754458
NCBI 1000 Genomes Browser:
rs1190754458
Molecular consequence:
  • NM_001170649.2:c.1231G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001170650.2:c.1105G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001375328.1:c.1282G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001375329.1:c.1282G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001375330.1:c.1282G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001375331.1:c.1231G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001375332.1:c.325G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001375333.1:c.1231G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001375334.1:c.1282G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001375335.1:c.1282G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001375336.1:c.1231G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001375337.1:c.1231G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_031206.7:c.1282G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NR_164681.1:n.1354G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:
Wilson-Turner syndrome (WTS)
Synonyms:
Mental retardation, X-linked, with gynecomastia and obesity; Wilson Turner mental retardation syndrome; Mental retardation, X-linked, syndromic 6; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0010665; MedGen: C1839736; Orphanet: 3459; OMIM: 309585

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001544804Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Jul 8, 2020) 		germlineclinical testing

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

SCV003816486Revvity Omics, Revvity
criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significance
(Nov 14, 2019) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
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

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 Invitae, SCV001544804.4

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

Description

This variant has not been reported in the literature in individuals with LAS1L-related conditions. This sequence change replaces valine with methionine at codon 428 of the LAS1L protein (p.Val428Met). The valine residue is weakly conserved and there is a small physicochemical difference between valine and methionine. This variant is not present in population databases (ExAC no frequency). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated, but these predictions have not been confirmed by published functional studies and their clinical significance is uncertain. 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 Revvity Omics, Revvity, SCV003816486.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Mar 16, 2024