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NM_015909.4(NBAS):c.1501C>T (p.Arg501Ter) AND Infantile liver failure syndrome 2

Germline classification:
Likely pathogenic (2 submissions)
Last evaluated:
May 18, 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:
RCV000755658.3

Allele description [Variation Report for NM_015909.4(NBAS):c.1501C>T (p.Arg501Ter)]

NM_015909.4(NBAS):c.1501C>T (p.Arg501Ter)

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.1501C>T (p.Arg501Ter)
HGVS:
  • NC_000002.12:g.15474165G>A
  • NG_032964.1:g.92184C>T
  • NM_015909.4:c.1501C>TMANE SELECT
  • NP_056993.2:p.Arg501Ter
  • NC_000002.11:g.15614289G>A
  • NM_015909.3:c.1501C>T
  • NR_052013.3:n.1531C>T
Protein change:
R501*
Links:
dbSNP: rs759960319
NCBI 1000 Genomes Browser:
rs759960319
Molecular consequence:
  • NR_052013.3:n.1531C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_015909.4:c.1501C>T - nonsense - [Sequence Ontology: SO:0001587]
Observations:
1

Condition(s)

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

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000882687Laboratory of Medical Genetics, University of Torino
no assertion criteria provided
Pathogenic
(Nov 7, 2018)
inheritedclinical testing

SCV002761519Genetics and Molecular Pathology, SA Pathology

See additional submitters

criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely pathogenic
(May 18, 2021)
germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedinheritedyes1not providednot providednot providednot providedclinical testing

Citations

PubMed

NBAS pathogenic variants: Defining the associated clinical and facial phenotype and genotype-phenotype correlations.

Carli D, Giorgio E, Pantaleoni F, Bruselles A, Barresi S, Riberi E, Licciardi F, Gazzin A, Baldassarre G, Pizzi S, Niceta M, Radio FC, Molinatto C, Montin D, Calvo PL, Ciolfi A, Fleischer N, Ferrero GB, Brusco A, Tartaglia M.

Hum Mutat. 2019 Jun;40(6):721-728. doi: 10.1002/humu.23734. Epub 2019 Mar 18.

PubMed [citation]
PMID:
30825388

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 Laboratory of Medical Genetics, University of Torino, SCV000882687.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided

Description

Found in compound heterozygosity with c.6840G>A

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1inheritedyesnot providednot providednot provided1not providednot providednot provided

From Genetics and Molecular Pathology, SA Pathology, SCV002761519.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

The NBAS c.1501C>T variant is a single nucleotide change which is predicted to result in premature termination of the protein product at codon 501 (PVS1). This variant has been identified in a patient with short stature, hypogammaglobinaemia, ocular involvement, and elevated liver transaminases (PMID:30825388) (PS4_mod). This variant is in dbSNP (rs759960319) but is rare in population databases (gnomAD 4/251424, 0 homozygotes). This variant has been reported in ClinVar as pathogenic for Infantile liver failure syndrome 2 by another diagnostic laboratory (ClinVar Variation ID: 609275). The NBAS c.1501C>T variant is classified as LIKELY PATHOGENIC (PS4_mod, PVS1)

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

Last Updated: Feb 28, 2024