NM_005198.5(CHKB):c.736+5_736+7del AND Megaconial type congenital muscular dystrophy

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jun 28, 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:: RCV002838730.3

Allele description [Variation Report for NM_005198.5(CHKB):c.736+5_736+7del]

NM_005198.5(CHKB):c.736+5_736+7del

Genes:

CHKB-CPT1B:CHKB-CPT1B readthrough (NMD candidate) [Gene - HGNC]
CHKB:choline kinase beta [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

22q13.33

Genomic location:

Preferred name:

NM_005198.5(CHKB):c.736+5_736+7del

HGVS:

NC_000022.11:g.50580353_50580355del
NG_012643.1:g.3315_3317del
NG_029213.1:g.7647_7649del
NM_005198.5:c.736+5_736+7delMANE SELECT
LRG_855:g.7647_7649del
NC_000022.10:g.51018780_51018782del
NC_000022.10:g.51018782_51018784del

Molecular consequence:

NM_005198.5:c.736+5_736+7del - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:: Megaconial type congenital muscular dystrophy (MDCMC)
Synonyms:: MUSCULAR DYSTROPHY, CONGENITAL, WITH MITOCHONDRIAL STRUCTURAL ABNORMALITIES; CHKB-Related Muscle Diseases
Identifiers:: MONDO: MONDO:0011246; MedGen: C1865233; Orphanet: 280671; OMIM: 602541

Recent activity

Clear Turn Off Turn On

uncharacterized protein TRIADDRAFT_54178 [Trichoplax adhaerens]
uncharacterized protein TRIADDRAFT_54178 [Trichoplax adhaerens]
gi|196000887|ref|XP_002110311.1|

Protein
hypothetical protein tlr2403 [Thermosynechococcus elongatus BP-1]
hypothetical protein tlr2403 [Thermosynechococcus elongatus BP-1]
gi|22299946|ref|NP_683193.1|

Protein
txid333[Organism] (2)
GEO DataSets
gem-associated protein 7 isoform X1 [Homo sapiens]
gem-associated protein 7 isoform X1 [Homo sapiens]
gi|2462567783|ref|XP_054178155.1|

Protein

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003212271	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jun 28, 2022)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 17576681, 9536098, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003212271

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jun 28, 2022)

germline

clinical testing

PubMed (3)
[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

Aberrant 5' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization.

Buratti E, Chivers M, Královicová J, Romano M, Baralle M, Krainer AR, Vorechovsky I.

Nucleic Acids Res. 2007;35(13):4250-63. Epub 2007 Jun 18.

PubMed [citation]

PMID:: 17576681
PMCID:: PMC1934990

Statistical features of human exons and their flanking regions.

Zhang MQ.

Hum Mol Genet. 1998 May;7(5):919-32.

PubMed [citation]

PMID:: 9536098

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003212271.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

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. Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. This variant has not been reported in the literature in individuals affected with CHKB-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change falls in intron 6 of the CHKB gene. It does not directly change the encoded amino acid sequence of the CHKB protein. It affects a nucleotide within the consensus splice site.

#	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

ClinVar

Relating variation to medicine