NC_000004.11:g.(?_38765721)_(41750627_?)dup AND Lipoic acid synthetase deficiency

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Oct 3, 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:: RCV003107887.11

Allele description [Variation Report for NC_000004.11:g.(?_38765721)_(41750627_?)dup]

NC_000004.11:g.(?_38765721)_(41750627_?)dup

Genes:

LIMCH1:LIM and calponin homology domains 1 [Gene - OMIM - HGNC]
N4BP2:NEDD4 binding protein 2 [Gene - OMIM - HGNC]
NSUN7:NOP2/Sun RNA methyltransferase family member 7 [Gene - OMIM - HGNC]
PDS5A:PDS5 cohesin associated factor A [Gene - OMIM - HGNC]
RBM47:RNA binding motif protein 47 [Gene - OMIM - HGNC]
UGDH:UDP-glucose 6-dehydrogenase [Gene - OMIM - HGNC]
WDR19:WD repeat domain 19 [Gene - OMIM - HGNC]
APBB2:amyloid beta precursor protein binding family B member 2 [Gene - OMIM - HGNC]
CHRNA9:cholinergic receptor nicotinic alpha 9 subunit [Gene - OMIM - HGNC]
FAM114A1:family with sequence similarity 114 member A1 [Gene - HGNC]
KLHL5:kelch like family member 5 [Gene - OMIM - HGNC]
KLB:klotho beta [Gene - OMIM - HGNC]
LIAS:lipoic acid synthetase [Gene - OMIM - HGNC]
PHOX2B:paired like homeobox 2B [Gene - OMIM - HGNC]
RHOH:ras homolog family member H [Gene - OMIM - HGNC]
RFC1:replication factor C subunit 1 [Gene - OMIM - HGNC]
RPL9:ribosomal protein L9 [Gene - OMIM - HGNC]
SMIM14:small integral membrane protein 14 [Gene - HGNC]
TLR10:toll like receptor 10 [Gene - OMIM - HGNC]
TLR1:toll like receptor 1 [Gene - OMIM - HGNC]
TLR6:toll like receptor 6 [Gene - OMIM - HGNC]
TMEM156:transmembrane protein 156 [Gene - HGNC]
UCHL1:ubiquitin C-terminal hydrolase L1 [Gene - OMIM - HGNC]
UBE2K:ubiquitin conjugating enzyme E2 K [Gene - OMIM - HGNC]

Variant type:

Duplication

Cytogenetic location:

4p14-13

Genomic location:

Chr4: 38765721 - 41750627 (on Assembly GRCh37)

Preferred name:

NC_000004.11:g.(?_38765721)_(41750627_?)dup

HGVS:

NC_000004.11:g.(?_38765721)_(41750627_?)dup

Condition(s)

Name:: Lipoic acid synthetase deficiency
Synonyms:: Pyruvate dehydrogenase lipoic acid synthetase deficiency; HYPERGLYCINEMIA, LACTIC ACIDOSIS, AND SEIZURES
Identifiers:: MONDO: MONDO:0013762; MedGen: C3280887; Orphanet: 401859; OMIM: 614462

Recent activity

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branched-chain-amino-acid aminotransferase, mitochondrial isoform X3 [Rattus nor...
branched-chain-amino-acid aminotransferase, mitochondrial isoform X3 [Rattus norvegicus]
gi|2678870650|ref|XP_063128813.1|

Protein
XK-related protein 3 [Homo sapiens]
XK-related protein 3 [Homo sapiens]
gi|103471991|ref|NP_787074.2|

Protein
branched-chain-amino-acid aminotransferase, mitochondrial precursor [Rattus norv...
branched-chain-amino-acid aminotransferase, mitochondrial precursor [Rattus norvegicus]
gi|1937369993|ref|NP_071795.2|

Protein
C1q and tumor necrosis factor related protein 3, isoform CRA_b [Homo sapiens]
C1q and tumor necrosis factor related protein 3, isoform CRA_b [Homo sapiens]
gi|119631225|gb|EAX10820.1||gnl|WGS |hCP1883668

Protein
similar to RIKEN cDNA 1600029D21 [Rattus norvegicus]
similar to RIKEN cDNA 1600029D21 [Rattus norvegicus]
gi|149041614|gb|EDL95455.1||gnl|WGS |rCP27002

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003791558	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Oct 3, 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

SCV003791558

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Oct 3, 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, SCV003791558.2

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

Description

A copy number gain of the genomic region encompassing the full coding sequence of the LIAS gene has been identified. The boundaries of this event are unknown as they extend beyond the assayed region for this gene and therefore may encompass additional genes. As the precise location of this event is unknown, it may be in tandem or it may be located elsewhere in the genome. This variant has not been reported in the literature in individuals affected with LIAS-related conditions. 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.

#	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: Nov 10, 2024

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