NC_000002.11:g.(?_236403331)_(242801596_?)del AND Bethlem myopathy 1A

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Oct 15, 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:: RCV003113452.4

Allele description [Variation Report for NC_000002.11:g.(?_236403331)_(242801596_?)del]

NC_000002.11:g.(?_236403331)_(242801596_?)del

Genes:

AGAP1:ArfGAP with GTPase domain, ankyrin repeat and PH domain 1 [Gene - OMIM - HGNC]
BOK:BCL2 family apoptosis regulator BOK [Gene - OMIM - HGNC]
COPS8:COP9 signalosome subunit 8 [Gene - OMIM - HGNC]
COPS9:COP9 signalosome subunit 9 [Gene - OMIM - HGNC]
D2HGDH:D-2-hydroxyglutarate dehydrogenase [Gene - OMIM - HGNC]
FARP2:FERM, ARH/RhoGEF and pleckstrin domain protein 2 [Gene - OMIM - HGNC]
GPR35:G protein-coupled receptor 35 [Gene - OMIM - HGNC]
ILKAP:ILK associated serine/threonine phosphatase [Gene - OMIM - HGNC]
IQCA1:IQ motif containing with AAA domain 1 [Gene - HGNC]
LRRFIP1:LRR binding FLII interacting protein 1 [Gene - OMIM - HGNC]
NDUFA10:NADH:ubiquinone oxidoreductase subunit A10 [Gene - OMIM - HGNC]
PASK:PAS domain containing serine/threonine kinase [Gene - OMIM - HGNC]
RAB17:RAB17, member RAS oncogene family [Gene - OMIM - HGNC]
RBM44:RNA binding motif protein 44 [Gene - HGNC]
THAP4:THAP domain containing 4 [Gene - OMIM - HGNC]
TRAF3IP1:TRAF3 interacting protein 1 [Gene - OMIM - HGNC]
AGXT:alanine--glyoxylate aminotransferase [Gene - OMIM - HGNC]
ANKMY1:ankyrin repeat and MYND domain containing 1 [Gene - OMIM - HGNC]
ASB18:ankyrin repeat and SOCS box containing 18 [Gene - HGNC]
ASB1:ankyrin repeat and SOCS box containing 1 [Gene - OMIM - HGNC]
ANO7:anoctamin 7 [Gene - OMIM - HGNC]
AQP12A:aquaporin 12A [Gene - OMIM - HGNC]
AQP12B:aquaporin 12B [Gene - HGNC]
RNPEPL1:arginyl aminopeptidase like 1 [Gene - OMIM - HGNC]
ACKR3:atypical chemokine receptor 3 [Gene - OMIM - HGNC]
ATG4B:autophagy related 4B cysteine peptidase [Gene - OMIM - HGNC]
CAPN10:calpain 10 [Gene - OMIM - HGNC]
COL6A3:collagen type VI alpha 3 chain [Gene - OMIM - HGNC]
DTYMK:deoxythymidylate kinase [Gene - OMIM - HGNC]
DUSP28:dual specificity phosphatase 28 [Gene - HGNC]
ERFE:erythroferrone [Gene - OMIM - HGNC]
ESPNL:espin like [Gene - OMIM - HGNC]
GAL3ST2:galactose-3-O-sulfotransferase 2 [Gene - OMIM - HGNC]
GBX2:gastrulation brain homeobox 2 [Gene - OMIM - HGNC]
GPC1:glypican 1 [Gene - OMIM - HGNC]
HES6:hes family bHLH transcription factor 6 [Gene - OMIM - HGNC]
HDLBP:high density lipoprotein binding protein [Gene - OMIM - HGNC]
HDAC4:histone deacetylase 4 [Gene - OMIM - HGNC]
ING5:inhibitor of growth family member 5 [Gene - OMIM - HGNC]
KLHL30:kelch like family member 30 [Gene - HGNC]
KIF1A:kinesin family member 1A [Gene - OMIM - HGNC]
MAB21L4:mab-21 like 4 [Gene - HGNC]
MLPH:melanophilin [Gene - OMIM - HGNC]
MIR149:microRNA 149 [Gene - OMIM - HGNC]
MTERF4:mitochondrial transcription termination factor 4 [Gene - OMIM - HGNC]
NEU4:neuraminidase 4 [Gene - OMIM - HGNC]
OR6B2:olfactory receptor family 6 subfamily B member 2 [Gene - HGNC]
OR6B3:olfactory receptor family 6 subfamily B member 3 [Gene - HGNC]
OTOS:otospiralin [Gene - OMIM - HGNC]
PER2:period circadian regulator 2 [Gene - OMIM - HGNC]
PDCD1:programmed cell death 1 [Gene - OMIM - HGNC]
PRLH:prolactin releasing hormone [Gene - OMIM - HGNC]
PRR21:proline rich 21 [Gene - HGNC]
PPP1R7:protein phosphatase 1 regulatory subunit 7 [Gene - OMIM - HGNC]
RAMP1:receptor activity modifying protein 1 [Gene - OMIM - HGNC]
SCLY:selenocysteine lyase [Gene - OMIM - HGNC]
SEPTIN2:septin 2 [Gene - OMIM - HGNC]
STK25:serine/threonine kinase 25 [Gene - OMIM - HGNC]
SNED1:sushi, nidogen and EGF like domains 1 [Gene - OMIM - HGNC]
TWIST2:twist family bHLH transcription factor 2 [Gene - OMIM - HGNC]
UBE2F:ubiquitin conjugating enzyme E2 F (putative) [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

2q37.2-37.3

Genomic location:

Chr2: 236403331 - 242801596 (on Assembly GRCh37)

Preferred name:

NC_000002.11:g.(?_236403331)_(242801596_?)del

HGVS:

NC_000002.11:g.(?_236403331)_(242801596_?)del

Condition(s)

Name:: Bethlem myopathy 1A
Synonyms:: Myopathy, benign congenital, with contractures; Bethlem myopathy 1
Identifiers:: MONDO: MONDO:0024530; MedGen: CN029274; Orphanet: 610; OMIM: 158810

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003793720	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Oct 15, 2022)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 26004199, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003793720

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Oct 15, 2022)

germline

clinical testing

PubMed (2)
[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

Recessive mutations in the α3 (VI) collagen gene COL6A3 cause early-onset isolated dystonia.

Zech M, Lam DD, Francescatto L, Schormair B, Salminen AV, Jochim A, Wieland T, Lichtner P, Peters A, Gieger C, Lochmüller H, Strom TM, Haslinger B, Katsanis N, Winkelmann J.

Am J Hum Genet. 2015 Jun 4;96(6):883-93. doi: 10.1016/j.ajhg.2015.04.010. Epub 2015 May 21.

PubMed [citation]

PMID:: 26004199
PMCID:: PMC4457951

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, SCV003793720.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

A gross deletion of the genomic region encompassing the full coding sequence of the COL6A3 gene has been identified. Loss-of-function variants in COL6A3 are known to be pathogenic (PMID: 26004199). The boundaries of this event are unknown as they extend beyond the assayed region for this gene and therefore may encompass additional genes. This variant has not been reported in the literature in individuals affected with COL6A3-related conditions. 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: Sep 29, 2024

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