NM_001242882.2(NAXD):c.542_565del (p.Arg181_Asn188del) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 16, 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:: RCV002857949.3

Allele description [Variation Report for NM_001242882.2(NAXD):c.542_565del (p.Arg181_Asn188del)]

NM_001242882.2(NAXD):c.542_565del (p.Arg181_Asn188del)

Gene:

NAXD:NAD(P)HX dehydratase [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

13q34

Genomic location:

Preferred name:

NM_001242882.2(NAXD):c.542_565del (p.Arg181_Asn188del)

HGVS:

NC_000013.11:g.110634721_110634744del
NG_128427.1:g.599_622del
NM_001242881.2:c.596_619del
NM_001242882.2:c.542_565delMANE SELECT
NM_001242883.2:c.266_289del
NM_018210.4:c.596_619del
NP_001229810.1:p.Arg199_Asn206del
NP_001229811.1:p.Arg181_Asn188del
NP_001229812.1:p.Arg89_Asn96del
NP_060680.2:p.Arg199_Asn206del
NC_000013.10:g.111287065_111287088del
NC_000013.10:g.111287068_111287091del
NR_040103.1:n.684_707del
NR_040104.1:n.595_618del

Molecular consequence:

NM_001242881.2:c.596_619del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001242882.2:c.542_565del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001242883.2:c.266_289del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_018210.4:c.596_619del - inframe_deletion - [Sequence Ontology: SO:0001822]
NR_040103.1:n.684_707del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_040104.1:n.595_618del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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Cladosporium hemileiicola strain COAD:2567 internal transcribed spacer 1, partia...
Cladosporium hemileiicola strain COAD:2567 internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene and internal transcribed spacer 2, complete sequence; and large subunit ribosomal RNA gene, partial sequence
gi|2309320229|gb|OP535376.1|

Nucleotide
translation elongation factor 1-alpha, partial [Cladosporium acalyphae]
translation elongation factor 1-alpha, partial [Cladosporium acalyphae]
gi|946525742|gb|ALM06154.1|

Protein
Cladosporium inversicolor strain CPC 14190 actin (act) gene, partial cds
Cladosporium inversicolor strain CPC 14190 actin (act) gene, partial cds
gi|309385290|gb|HM148595.1|

Nucleotide
Cladosporium inversicolor strain CBS 464.82 translation elongation factor 1-alph...
Cladosporium inversicolor strain CBS 464.82 translation elongation factor 1-alpha (tef1) gene, partial cds
gi|309384792|gb|HM148346.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003229686	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Aug 16, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003229686

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Aug 16, 2022)

germline

clinical testing

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

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

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003229686.2

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

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. This variant has not been reported in the literature in individuals affected with NAXD-related conditions. This variant is not present in population databases (gnomAD no frequency). This variant, c.596_619del, results in the deletion of 8 amino acid(s) of the NAXD protein (p.Arg199_Asn206del), but otherwise preserves the integrity of the reading frame.

#	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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