NM_015909.4(NBAS):c.2827G>T (p.Glu943Ter) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Dec 11, 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:: RCV001390101.4

Allele description [Variation Report for NM_015909.4(NBAS):c.2827G>T (p.Glu943Ter)]

NM_015909.4(NBAS):c.2827G>T (p.Glu943Ter)

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.2827G>T (p.Glu943Ter)

HGVS:

NC_000002.12:g.15415656C>A
NG_032964.1:g.150693G>T
NM_015909.4:c.2827G>TMANE SELECT
NP_056993.2:p.Glu943Ter
NC_000002.11:g.15555780C>A
NR_052013.3:n.2857G>T

Protein change:

E943*

Links:

dbSNP: rs143012720

NCBI 1000 Genomes Browser:

rs143012720

Molecular consequence:

NR_052013.3:n.2857G>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_015909.4:c.2827G>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001591722	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Dec 11, 2023)	germline	clinical testing	PubMed (6) [See all records that cite these PMIDs] 26541327, 27789416, 26073778, 28031453, 31761904, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001591722

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Dec 11, 2023)

germline

clinical testing

PubMed (6)
[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

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

Compound heterozygous variants in NBAS as a cause of atypical osteogenesis imperfecta.

Balasubramanian M, Hurst J, Brown S, Bishop NJ, Arundel P, DeVile C, Pollitt RC, Crooks L, Longman D, Caceres JF, Shackley F, Connolly S, Payne JH, Offiah AC, Hughes D; DDD Study., Parker MJ, Hide W, Skerry TM.

Bone. 2017 Jan;94:65-74. doi: 10.1016/j.bone.2016.10.023. Epub 2016 Oct 24.

PubMed [citation]

PMID:: 27789416
PMCID:: PMC6067660

See all PubMed Citations (6)

Details of each submission

From Invitae, SCV001591722.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (6)

Description

This sequence change creates a premature translational stop signal (p.Glu943*) 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). This variant is present in population databases (rs143012720, gnomAD 0.01%). This premature translational stop signal has been observed in individuals with SOPH syndrome and acute liver failure (PMID: 26073778, 28031453, 31761904). ClinVar contains an entry for this variant (Variation ID: 1076261). For these reasons, this variant has been classified as Pathogenic.

#	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: Feb 20, 2024

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