NM_005499.3(UBA2):c.800T>A (p.Leu267Ter) AND Chromosome 19q13.11 deletion syndrome, distal

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Sep 10, 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:: RCV001255700.1

Allele description [Variation Report for NM_005499.3(UBA2):c.800T>A (p.Leu267Ter)]

NM_005499.3(UBA2):c.800T>A (p.Leu267Ter)

Gene:

UBA2:ubiquitin like modifier activating enzyme 2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

19q13.11

Genomic location:

Preferred name:

NM_005499.3(UBA2):c.800T>A (p.Leu267Ter)

HGVS:

NC_000019.10:g.34450293T>A
NM_005499.3:c.800T>AMANE SELECT
NP_005490.1:p.Leu267Ter
NC_000019.9:g.34941198T>A
NM_005499.2:c.800T>A

Protein change:

L267*

Links:

dbSNP: rs2075478466

NCBI 1000 Genomes Browser:

rs2075478466

Molecular consequence:

NM_005499.3:c.800T>A - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:: Chromosome 19q13.11 deletion syndrome, distal
Identifiers:: MONDO: MONDO:0700107; MedGen: C4311048; OMIM: 613026

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001432255	NEI Ophthalmic Genomics Laboratory, National Institutes of Health	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Sep 10, 2020)	germline	research	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001432255

NEI Ophthalmic Genomics Laboratory, National Institutes of Health

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Sep 10, 2020)

germline

research

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	yes	not provided	not provided	not provided	not provided	not provided	research

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 NEI Ophthalmic Genomics Laboratory, National Institutes of Health, SCV001432255.1

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

Description

The variant NM_005499.2:c.800T>A (p.Leu267Ter) in the UBA2 gene has not been previously studied. We found this variant in 1 patient whereas it was absent in parental samples in a research study (Schnur, Yousaf, Liu et al, 2020). This variant is not listed in dbSNP, ClinVar and HGMD. It is absent in gnomAD browser. We invoked ACMG criteria [PVS1, PM2, PM6] and classified NM_005499.2:c.800T>A in the UBA2 gene as a Pathogenic mutation.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Apr 23, 2022

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