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NC_000002.11:g.(15378811_15415607)_(15567919_15601324)del AND Acute infantile liver failure due to synthesis defect of mtDNA-encoded proteins

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Apr 22, 2022
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:
RCV002238645.1

Allele description [Variation Report for NC_000002.11:g.(15378811_15415607)_(15567919_15601324)del]

NC_000002.11:g.(15378811_15415607)_(15567919_15601324)del

Gene:
NBAS:NBAS subunit of NRZ tethering complex [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
2p24.3
Genomic location:
Chr2: 15378811 - 15601324 (on Assembly GRCh37)
Preferred name:
NC_000002.11:g.(15378811_15415607)_(15567919_15601324)del
HGVS:
NC_000002.11:g.(15378811_15415607)_(15567919_15601324)del

Condition(s)

Name:
Acute infantile liver failure due to synthesis defect of mtDNA-encoded proteins
Synonyms:
Liver failure acute infantile; LIVER FAILURE, INFANTILE, TRANSIENT
Identifiers:
MONDO: MONDO:0013111; MedGen: C3278664; Orphanet: 217371; OMIM: 613070

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002511823Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)		Likely pathogenic
(Apr 22, 2022) 		germlineclinical testing

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV002511823.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

Variant summary: The variant identified by MLPA or other technology involves the deletion of exons 22-44 in the NBAS gene. A presumed nomenclature of c.(2339+1_2340-1)_(5724+1_5725-1)del has been designated for the purposes of this classification. Although exact breakpoints of this deletion are not known, it is expected to result in a large deletion, causing a frameshift in the NBAS gene, a known mechanism of disease. The variant was absent in 21694 control chromosomes (gnomAD database, structural variants dataset). To our knowledge, no occurrence of c.(2339+1_2340-1)_(5724+1_5725-1)del in individuals affected with Liver Failure Acute Infantile, Type 2 and no experimental evidence demonstrating its impact on protein function have been reported. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as likely pathogenic.

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

Last Updated: May 24, 2022