NM_015909.4(NBAS):c.3046G>T (p.Glu1016Ter) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jun 20, 2023
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:: RCV003545265.2

Allele description [Variation Report for NM_015909.4(NBAS):c.3046G>T (p.Glu1016Ter)]

NM_015909.4(NBAS):c.3046G>T (p.Glu1016Ter)

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.3046G>T (p.Glu1016Ter)

HGVS:

NC_000002.12:g.15402193C>A
NG_032964.1:g.164156G>T
NG_032964.2:g.164141G>T
NM_015909.4:c.3046G>TMANE SELECT
NP_056993.2:p.Glu1016Ter
NC_000002.11:g.15542317C>A
NR_052013.3:n.3076G>T

Protein change:

E1016*

Molecular consequence:

NR_052013.3:n.3076G>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_015909.4:c.3046G>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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PREDICTED: Acanthaster planci delta-sarcoglycan-like (LOC110989363), mRNA
PREDICTED: Acanthaster planci delta-sarcoglycan-like (LOC110989363), mRNA
gi|1229190947|ref|XM_022253691.1|

Nucleotide
PREDICTED: Homo sapiens phospholipase C eta 1 (PLCH1), transcript variant X11, m...
PREDICTED: Homo sapiens phospholipase C eta 1 (PLCH1), transcript variant X11, mRNA
gi|2217342705|ref|XM_005247239.2|

Nucleotide
1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase eta-1 isoform e [Homo ...
1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase eta-1 isoform e [Homo sapiens]
gi|1154067809|ref|NP_001336181.1|

Protein
1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase eta-1 isoform X1 [Homo...
1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase eta-1 isoform X1 [Homo sapiens]
gi|2462588178|ref|XP_054201714.1|

Protein
PREDICTED: Homo sapiens microtubule associated protein 2 (MAP2), transcript vari...
PREDICTED: Homo sapiens microtubule associated protein 2 (MAP2), transcript variant X14, mRNA
gi|2462573345|ref|XM_054342096.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004259791	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jun 20, 2023)	germline	clinical testing	PubMed (5) [See all records that cite these PMIDs] 26073778, 26541327, 27789416, 28031453, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004259791

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jun 20, 2023)

germline

clinical testing

PubMed (5)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Biallelic Mutations in NBAS Cause Recurrent Acute Liver Failure with Onset in Infancy.

Haack TB, Staufner C, Köpke MG, Straub BK, Kölker S, Thiel C, Freisinger P, Baric I, McKiernan PJ, Dikow N, Harting I, Beisse F, Burgard P, Kotzaeridou U, Kühr J, Himbert U, Taylor RW, Distelmaier F, Vockley J, Ghaloul-Gonzalez L, Zschocke J, Kremer LS, et al.

Am J Hum Genet. 2015 Jul 2;97(1):163-9. doi: 10.1016/j.ajhg.2015.05.009. Epub 2015 Jun 11.

PubMed [citation]

PMID:: 26073778
PMCID:: PMC4572578

Recurrent acute liver failure due to NBAS deficiency: phenotypic spectrum, disease mechanisms, and therapeutic concepts.

Staufner C, Haack TB, Köpke MG, Straub BK, Kölker S, Thiel C, Freisinger P, Baric I, McKiernan PJ, Dikow N, Harting I, Beisse F, Burgard P, Kotzaeridou U, Lenz D, Kühr J, Himbert U, Taylor RW, Distelmaier F, Vockley J, Ghaloul-Gonzalez L, Ozolek JA, et al.

J Inherit Metab Dis. 2016 Jan;39(1):3-16. doi: 10.1007/s10545-015-9896-7. Epub 2015 Nov 5.

PubMed [citation]

PMID:: 26541327

See all PubMed Citations (5)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004259791.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (5)

Description

This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Glu1016*) in the NBAS gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in NBAS are known to be pathogenic (PMID: 26073778, 26541327, 27789416, 28031453). For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals affected with NBAS-related conditions.

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

Last Updated: Sep 29, 2024

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