NM_001130987.2(DYSF):c.5830C>T (p.Arg1944Ter) AND not provided

Germline classification:: Pathogenic (4 submissions)
Last evaluated:: Dec 13, 2023
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000080312.16

Allele description [Variation Report for NM_001130987.2(DYSF):c.5830C>T (p.Arg1944Ter)]

NM_001130987.2(DYSF):c.5830C>T (p.Arg1944Ter)

Gene:

DYSF:dysferlin [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

2p13.2

Genomic location:

Preferred name:

NM_001130987.2(DYSF):c.5830C>T (p.Arg1944Ter)

Other names:

6086C>T

HGVS:

NC_000002.12:g.71674242C>T
NG_008694.1:g.225620C>T
NM_001130455.2:c.5716C>T
NM_001130976.2:c.5671C>T
NM_001130977.2:c.5734C>T
NM_001130978.2:c.5776C>T
NM_001130979.2:c.5806C>T
NM_001130980.2:c.5764C>T
NM_001130981.2:c.5827C>T
NM_001130982.2:c.5809C>T
NM_001130983.2:c.5779C>T
NM_001130984.2:c.5737C>T
NM_001130985.2:c.5767C>T
NM_001130986.2:c.5674C>T
NM_001130987.2:c.5830C>TMANE SELECT
NM_003494.4:c.5713C>T
NP_001123927.1:p.Arg1906Ter
NP_001124448.1:p.Arg1891Ter
NP_001124449.1:p.Arg1912Ter
NP_001124450.1:p.Arg1926Ter
NP_001124451.1:p.Arg1936Ter
NP_001124452.1:p.Arg1922Ter
NP_001124453.1:p.Arg1943Ter
NP_001124454.1:p.Arg1937Ter
NP_001124455.1:p.Arg1927Ter
NP_001124456.1:p.Arg1913Ter
NP_001124457.1:p.Arg1923Ter
NP_001124458.1:p.Arg1892Ter
NP_001124459.1:p.Arg1944Ter
NP_003485.1:p.Arg1905Ter
LRG_845t1:c.5713C>T
LRG_845t2:c.5830C>T
LRG_845:g.225620C>T
LRG_845p1:p.Arg1905Ter
LRG_845p2:p.Arg1944Ter
NC_000002.11:g.71901372C>T
NM_001130987.2:c.5830C>T
NM_003494.3:c.5713C>T
NP_003485.1:p.Arg1905*

Protein change:

R1891*; ARG1905TER

Links:

OMIM: 603009.0012; dbSNP: rs121908959

NCBI 1000 Genomes Browser:

rs121908959

Molecular consequence:

NM_001130455.2:c.5716C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001130976.2:c.5671C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001130977.2:c.5734C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001130978.2:c.5776C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001130979.2:c.5806C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001130980.2:c.5764C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001130981.2:c.5827C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001130982.2:c.5809C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001130983.2:c.5779C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001130984.2:c.5737C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001130985.2:c.5767C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001130986.2:c.5674C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001130987.2:c.5830C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_003494.4:c.5713C>T - nonsense - [Sequence Ontology: SO:0001587]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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Ceratotherium simum simum
Ceratotherium simum simum
Ceratotherium simum simum RefSeq Genome

BioProject
Arabidopsis thaliana Pectin lyase-like superfamily protein (QRT3), mRNA
Arabidopsis thaliana Pectin lyase-like superfamily protein (QRT3), mRNA
gi|42566976|ref|NM_118124.3|

Nucleotide
rpmE [Leptospira interrogans serovar Lai str. 56601]
rpmE [Leptospira interrogans serovar Lai str. 56601]
Gene ID:1150363

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000335577	Eurofins Ntd Llc (ga)	criteria provided, single submitter (EGL Classification Definitions 2015)	Pathogenic (Sep 22, 2015)	germline	clinical testing	Citation Link,
SCV000613217	Athena Diagnostics	criteria provided, single submitter (Athena Diagnostics Criteria)	Pathogenic (Mar 7, 2023)	unknown	clinical testing	PubMed (13) [See all records that cite these PMIDs] 16087766, 17070050, 16010686, 17698709, 18853459, 20544924, 22297152, 26916285, 24488599, 20558759, 27602406, 27066573, 26467025
SCV000680751	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Mar 24, 2023)	germline	clinical testing	Citation Link,
SCV002021876	Revvity Omics, Revvity	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Dec 13, 2023)	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	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	4	not provided	not provided	not provided	not provided	clinical testing
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Identification of a novel founder mutation in the DYSF gene causing clinical variability in the Spanish population.

Vilchez JJ, Gallano P, Gallardo E, Lasa A, Rojas-García R, Freixas A, De Luna N, Calafell F, Sevilla T, Mayordomo F, Baiget M, Illa I.

Arch Neurol. 2005 Aug;62(8):1256-9.

PubMed [citation]

PMID:: 16087766

Dysferlin expression in monocytes: a source of mRNA for mutation analysis.

De Luna N, Freixas A, Gallano P, Caselles L, Rojas-García R, Paradas C, Nogales G, Dominguez-Perles R, Gonzalez-Quereda L, Vílchez JJ, Márquez C, Bautista J, Guerrero A, Salazar JA, Pou A, Illa I, Gallardo E.

Neuromuscul Disord. 2007 Jan;17(1):69-76. Epub 2006 Oct 27.

PubMed [citation]

PMID:: 17070050

See all PubMed Citations (14)

Details of each submission

From Eurofins Ntd Llc (ga), SCV000335577.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	4	not provided	not provided	clinical testing	not provided

#	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		4	not provided	not provided	not provided

From Athena Diagnostics, SCV000613217.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (13)

Description

This variant is expected to result in the loss of a functional protein. The frequency of this variant in the general population is consistent with pathogenicity (http://gnomad.broadinstitute.org). In multiple individuals with Miyoshi muscular dystrophy, this variant has been seen with a single recessive pathogenic variant in the same gene, suggesting this variant may also be pathogenic. This variant is a common founder originating from Sueca, Spain (PMID: 16087766).

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

From GeneDx, SCV000680751.3

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

Description

Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss of function is a known mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 25525159, 16010686, 32400077, 33250842, 33215690, 30919934, 33715265, 31069529, 34559919, 33348118, 33610434, 20558759, 16087766)

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

From Revvity Omics, Revvity, SCV002021876.3

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

#	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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