NM_001211.6(BUB1B):c.3105A>C (p.Leu1035Phe) AND Mosaic variegated aneuploidy syndrome 1

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jun 2, 2021
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:: RCV001870171.6

Allele description [Variation Report for NM_001211.6(BUB1B):c.3105A>C (p.Leu1035Phe)]

NM_001211.6(BUB1B):c.3105A>C (p.Leu1035Phe)

Genes:

BUB1B:BUB1 mitotic checkpoint serine/threonine kinase B [Gene - OMIM - HGNC]
BUB1B-PAK6:BUB1B-PAK6 readthrough [Gene - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

15q15.1

Genomic location:

Preferred name:

NM_001211.6(BUB1B):c.3105A>C (p.Leu1035Phe)

HGVS:

NC_000015.10:g.40220711A>C
NG_016338.1:g.64703A>C
NG_033169.1:g.8284A>C
NM_001128628.3:c.-201+3044A>C
NM_001128629.3:c.-118+3044A>C
NM_001211.6:c.3105A>CMANE SELECT
NP_001202.4:p.Leu1035Phe
NP_001202.5:p.Leu1035Phe
LRG_489t1:c.3105A>C
LRG_489:g.64703A>C
LRG_489p1:p.Leu1035Phe
NC_000015.9:g.40512912A>C
NM_001211.5:c.3105A>C

Protein change:

L1035F

Links:

dbSNP: rs576684184

NCBI 1000 Genomes Browser:

rs576684184

Molecular consequence:

NM_001128628.3:c.-201+3044A>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001128629.3:c.-118+3044A>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001211.6:c.3105A>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Mosaic variegated aneuploidy syndrome 1 (MVA1)
Synonyms:: Warburton-Anyane-Yeboa syndrome
Identifiers:: MONDO: MONDO:0009759; MedGen: C1850343; Orphanet: 1052; OMIM: 257300

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002120908	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jun 2, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002120908

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jun 2, 2021)

germline

clinical testing

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

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

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, SCV002120908.3

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

Description

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. Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The phenylalanine amino acid residue is found in multiple mammalian species, suggesting that this missense change does not adversely affect protein function. These predictions have not been confirmed by published functional studies and their clinical significance is uncertain. This variant has not been reported in the literature in individuals with BUB1B-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change replaces leucine with phenylalanine at codon 1035 of the BUB1B protein (p.Leu1035Phe). The leucine residue is weakly conserved and there is a small physicochemical difference between leucine and phenylalanine.

#	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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