NM_001368882.1(COL13A1):c.1619del (p.Asn540fs) AND Congenital myasthenic syndrome 19

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jul 27, 2021
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

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:: RCV001543596.1

Allele description [Variation Report for NM_001368882.1(COL13A1):c.1619del (p.Asn540fs)]

NM_001368882.1(COL13A1):c.1619del (p.Asn540fs)

Gene:

COL13A1:collagen type XIII alpha 1 chain [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

10q22.1

Genomic location:

Preferred name:

NM_001368882.1(COL13A1):c.1619del (p.Asn540fs)

HGVS:

NC_000010.11:g.69930488del
NG_046344.1:g.133601del
NM_001130103.2:c.1586del
NM_001320951.2:c.1556del
NM_001368882.1:c.1619delMANE SELECT
NM_001368883.1:c.1583del
NM_001368884.1:c.1556del
NM_001368885.1:c.1520del
NM_001368886.1:c.956del
NM_001368895.1:c.1529del
NM_001368896.1:c.1415del
NM_001368897.1:c.1442del
NM_001368898.1:c.1415del
NM_080798.4:c.1415del
NM_080800.4:c.1529del
NM_080801.4:c.1520del
NM_080802.4:c.1520del
NM_080805.4:c.1433del
NP_001123575.1:p.Asn529fs
NP_001307880.1:p.Asn519fs
NP_001355811.1:p.Asn540fs
NP_001355812.1:p.Asn528fs
NP_001355813.1:p.Asn519fs
NP_001355814.1:p.Asn507fs
NP_001355815.1:p.Asn319fs
NP_001355824.1:p.Asn510fs
NP_001355825.1:p.Asn472fs
NP_001355826.1:p.Asn481fs
NP_001355827.1:p.Asn472fs
NP_542988.3:p.Asn472fs
NP_542990.3:p.Asn510fs
NP_542991.3:p.Asn507fs
NP_542992.3:p.Asn507fs
NP_542995.3:p.Asn478fs
NC_000010.10:g.71690244del
NM_001368882.1:c.1619delAMANE SELECT

Nucleotide change:

1-BP DEL, 1619A

Protein change:

N319fs

Links:

OMIM: 120350.0005; dbSNP: rs2135829327

NCBI 1000 Genomes Browser:

rs2135829327

Molecular consequence:

NM_001130103.2:c.1586del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001320951.2:c.1556del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001368882.1:c.1619del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001368883.1:c.1583del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001368884.1:c.1556del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001368885.1:c.1520del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001368886.1:c.956del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001368895.1:c.1529del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001368896.1:c.1415del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001368897.1:c.1442del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001368898.1:c.1415del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_080798.4:c.1415del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_080800.4:c.1529del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_080801.4:c.1520del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_080802.4:c.1520del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_080805.4:c.1433del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:: Congenital myasthenic syndrome 19
Identifiers:: MONDO: MONDO:0014745; MedGen: C4225235; Orphanet: 590; OMIM: 616720

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001762273	OMIM	no assertion criteria provided	Pathogenic (Jul 27, 2021)	germline	literature only	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001762273

OMIM

no assertion criteria provided

Pathogenic
(Jul 27, 2021)

germline

literature only

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	not provided	not provided	not provided	not provided	not provided	not provided	literature only

Citations

PubMed

Congenital myasthenic syndrome caused by novel COL13A1 mutations.

Dusl M, Moreno T, Munell F, Macaya A, Gratacòs M, Abicht A, Strom TM, Lochmüller H, Senderek J.

J Neurol. 2019 May;266(5):1107-1112. doi: 10.1007/s00415-019-09239-7. Epub 2019 Feb 14.

PubMed [citation]

PMID:: 30767057

Details of each submission

From OMIM, SCV001762273.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	literature only	PubMed (1)

Description

In 2 German sibs, born to consanguineous parents, with congenital myasthenic syndrome-19 (CMS19; 616720), Dusl et al. (2019) identified homozygosity for a 1-bp deletion (c.1619delA) in the COL13A1 gene, predicted to result in a frameshift at residue glu543 in the COLI-3 collagenous domain. The mutation, which was identified by whole-exome sequencing and confirmed by Sanger sequencing, segregated with disease in the family. The variant was not present in the gnomAD, EVS, and dbSNP databases. Functional studies were not performed.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	not provided	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Dec 24, 2023

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