NM_015909.4(NBAS):c.3502G>A (p.Glu1168Lys) AND Infantile liver failure syndrome 2

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 28, 2019
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:: RCV002471098.1

Allele description [Variation Report for NM_015909.4(NBAS):c.3502G>A (p.Glu1168Lys)]

NM_015909.4(NBAS):c.3502G>A (p.Glu1168Lys)

Gene:

NBAS:NBAS subunit of NRZ tethering complex [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

2p24.3

Genomic location:

Preferred name:

NM_015909.4(NBAS):c.3502G>A (p.Glu1168Lys)

HGVS:

NC_000002.12:g.15379690C>T
NG_032964.1:g.186659G>A
NM_015909.4:c.3502G>AMANE SELECT
NP_056993.2:p.Glu1168Lys
NC_000002.11:g.15519814C>T
NM_015909.2:c.3502G>A
NM_015909.3:c.3502G>A
NR_052013.3:n.3532G>A

Protein change:

E1168K

Links:

dbSNP: rs140855946

NCBI 1000 Genomes Browser:

rs140855946

Molecular consequence:

NM_015909.4:c.3502G>A - missense variant - [Sequence Ontology: SO:0001583]
NR_052013.3:n.3532G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Infantile liver failure syndrome 2 (ILFS2)
Identifiers:: MONDO: MONDO:0014659; MedGen: C3809651; OMIM: 616483

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002768532	Victorian Clinical Genetics Services, Murdoch Childrens Research Institute See additional submitters Shariant Australia, Australian Genomics	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Aug 28, 2019)	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

SCV002768532

Victorian Clinical Genetics Services, Murdoch Childrens Research Institute

See additional submitters

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Aug 28, 2019)

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	yes	not provided	not provided	not provided	not provided	not provided	clinical 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, SCV002768532.1

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

Description

A heterozygous missense variant was identified, NM_015909.3(NBAS):c.3502G>A in exon 30 of 52 of the NBAS gene. This substitution is predicted to create a minor amino acid change from glutamic acid to lysine at position 1168 of the protein, NP_056993.2(NBAS):p.(Glu1168Lys). The glutamic acid at this position has low conservation (100 vertebrates, UCSC), but is located within the Sec39 functional domain. In silico software predicts this variant to be benign (PolyPhen, SIFT, CADD, MutationTaster). The variant is present in the gnomAD population database at a frequency of 0.03% (89 heterozygotes; 0 homozygotes). The variant has not previously been reported in clinical cases. Based on information available at the time of curation, this variant has been classified as a VARIANT of UNCERTAIN SIGNIFICANCE (VUS) with LOW CLINICAL RELEVANCE.

#	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: May 1, 2024

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