NM_015909.4(NBAS):c.2950del (p.Ile984fs) AND Infantile liver failure

Clinical significance:Pathogenic (Last evaluated: Sep 1, 2017)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000602655.1

Allele description [Variation Report for NM_015909.4(NBAS):c.2950del (p.Ile984fs)]

NM_015909.4(NBAS):c.2950del (p.Ile984fs)

Gene:
NBAS:NBAS subunit of NRZ tethering complex [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
2p24.3
Genomic location:
Preferred name:
NM_015909.4(NBAS):c.2950del (p.Ile984fs)
HGVS:
  • NC_000002.12:g.15402294del
  • NG_032964.1:g.164060del
  • NM_015909.4:c.2950delMANE SELECT
  • NP_056993.2:p.Ile984fs
  • NC_000002.11:g.15542413delT
  • NC_000002.11:g.15542418del
  • NM_015909.3:c.2950delA
  • NR_052013.3:n.2980del
  • p.Ile984LeufsX8
Protein change:
I984fs
Links:
dbSNP: rs776797592
NCBI 1000 Genomes Browser:
rs776797592
Molecular consequence:
  • NM_015909.4:c.2950del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NR_052013.3:n.2980del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
Observations:
1

Condition(s)

Name:
Infantile liver failure
Synonyms:
Infantile liver failure syndrome; Fever-associated acute infantile liver failure syndrome
Identifiers:
MONDO: MONDO:0000023; MedGen: CN228161; Orphanet: 464724; OMIM: PS615438

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000712173Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicinecriteria provided, single submitter
Pathogenic
(Sep 1, 2017)
germlineclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot provided11not providednot providednot providedclinical testing

Citations

PubMed

A systematic approach to assessing the clinical significance of genetic variants.

Duzkale H, Shen J, McLaughlin H, Alfares A, Kelly MA, Pugh TJ, Funke BH, Rehm HL, Lebo MS.

Clin Genet. 2013 Nov;84(5):453-63. doi: 10.1111/cge.12257.

PubMed [citation]
PMID:
24033266
PMCID:
PMC3995020

Details of each submission

From Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, SCV000712173.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (1)

Description

The p.Ile984LeufsX8 variant in NBAS has not been reported in individuals with di sease and has been identified in 9/120,878 of chromosomes by the Exome Aggregati on Consortium (ExAC, http://exac.broadinstitute.org; dbSNP rs140841721). Althou gh this variant has been seen in the general population, its frequency is low en ough to be consistent with a recessive carrier frequency. This variant is predic ted to cause a frameshift, which alters the protein?s amino acid sequence beginn ing at position 984 and leads to a premature termination codon 8 amino acids dow nstream. This alteration is then predicted to lead to a truncated or absent prot ein. Homozygous or compound heterozygous mutations in NBAS have been associated with Infantile liver failure syndrome 2. In summary, this variant meets our cr iteria to be classified as pathogenic for Infantile liver failure syndrome 2 in an autosomal recessive manner based on low frequency in controls and functional prediction

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

Last Updated: Jul 7, 2021

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