NM_001130987.2(DYSF):c.3167G>A (p.Arg1056Gln) AND Distal myopathy with anterior tibial onset

Germline classification:: Likely pathogenic (2 submissions)
Last evaluated:: Mar 21, 2019
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:: RCV001196058.11

Allele description [Variation Report for NM_001130987.2(DYSF):c.3167G>A (p.Arg1056Gln)]

NM_001130987.2(DYSF):c.3167G>A (p.Arg1056Gln)

Gene:

DYSF:dysferlin [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

2p13.2

Genomic location:

Preferred name:

NM_001130987.2(DYSF):c.3167G>A (p.Arg1056Gln)

Other names:

NM_001130455.1(DYSF):c.3116G>A(p.Arg1039Gln); NM_001130976.1(DYSF):c.3071G>A(p.Arg1024Gln); NM_001130977.1(DYSF):c.3071G>A(p.Arg1024Gln); NM_001130978.1(DYSF):c.3113G>A(p.Arg1038Gln); NM_001130979.1(DYSF):c.3206G>A(p.Arg1069Gln); NM_001130980.1(DYSF):c.3164G>A(p.Arg1055Gln); NM_001130981.1(DYSF):c.3164G>A(p.Arg1055Gln); NM_001130982.1(DYSF):c.3209G>A(p.Arg1070Gln); NM_001130983.1(DYSF):c.3116G>A(p.Arg1039Gln); NM_001130984.1(DYSF):c.3074G>A(p.Arg1025Gln); NM_001130985.1(DYSF):c.3167G>A(p.Arg1056Gln); NM_001130986.1(DYSF):c.3074G>A(p.Arg1025Gln); NM_001130987.1(DYSF):c.3167G>A(p.Arg1056Gln); NM_003494.3(DYSF):c.3113G>A(p.Arg1038Gln)

HGVS:

NC_000002.12:g.71570680G>A
NG_008694.1:g.122058G>A
NM_001130455.2:c.3116G>A
NM_001130976.2:c.3071G>A
NM_001130977.2:c.3071G>A
NM_001130978.2:c.3113G>A
NM_001130979.2:c.3206G>A
NM_001130980.2:c.3164G>A
NM_001130981.2:c.3164G>A
NM_001130982.2:c.3209G>A
NM_001130983.2:c.3116G>A
NM_001130984.2:c.3074G>A
NM_001130985.2:c.3167G>A
NM_001130986.2:c.3074G>A
NM_001130987.2:c.3167G>AMANE SELECT
NM_003494.4:c.3113G>A
NP_001123927.1:p.Arg1039Gln
NP_001124448.1:p.Arg1024Gln
NP_001124449.1:p.Arg1024Gln
NP_001124450.1:p.Arg1038Gln
NP_001124451.1:p.Arg1069Gln
NP_001124452.1:p.Arg1055Gln
NP_001124453.1:p.Arg1055Gln
NP_001124454.1:p.Arg1070Gln
NP_001124455.1:p.Arg1039Gln
NP_001124456.1:p.Arg1025Gln
NP_001124457.1:p.Arg1056Gln
NP_001124458.1:p.Arg1025Gln
NP_001124459.1:p.Arg1056Gln
NP_003485.1:p.Arg1038Gln
LRG_845t1:c.3113G>A
LRG_845t2:c.3167G>A
LRG_845:g.122058G>A
LRG_845p1:p.Arg1038Gln
LRG_845p2:p.Arg1056Gln
NC_000002.11:g.71797810G>A
NM_001130987.1:c.3167G>A
NM_001130987.2:c.3167G>A
NM_003494.3:c.3113G>A
O75923:p.Arg1038Gln

Protein change:

R1024Q

Links:

UniProtKB: O75923#VAR_024862; dbSNP: rs150877497

NCBI 1000 Genomes Browser:

rs150877497

Molecular consequence:

NM_001130455.2:c.3116G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001130976.2:c.3071G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001130977.2:c.3071G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001130978.2:c.3113G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001130979.2:c.3206G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001130980.2:c.3164G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001130981.2:c.3164G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001130982.2:c.3209G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001130983.2:c.3116G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001130984.2:c.3074G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001130985.2:c.3167G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001130986.2:c.3074G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001130987.2:c.3167G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_003494.4:c.3113G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Distal myopathy with anterior tibial onset
Identifiers:: MONDO: MONDO:0011721; MedGen: C1847532; Orphanet: 178400; OMIM: 606768

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001366487	Centre for Mendelian Genomics, University Medical Centre Ljubljana	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Mar 21, 2019)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV005091514	Solve-RD Consortium	no assertion criteria provided	Likely pathogenic (Jun 1, 2022)	inherited	provider interpretation

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001366487

Centre for Mendelian Genomics, University Medical Centre Ljubljana

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Mar 21, 2019)

unknown

clinical testing

PubMed (1)
[See all records that cite this PMID]

SCV005091514

Solve-RD Consortium

no assertion criteria provided

Likely pathogenic
(Jun 1, 2022)

inherited

provider interpretation

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	inherited	yes	not provided	not provided	not provided	not provided	not provided	provider interpretation
not provided	unknown	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Centre for Mendelian Genomics, University Medical Centre Ljubljana, SCV001366487.2

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

Description

This variant was classified as: Likely pathogenic. The following ACMG criteria were applied in classifying this variant: PS1,PM2,PP3. This variant was detected in homozygous state.

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

From Solve-RD Consortium, SCV005091514.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	provider interpretation	not provided

Description

Variant confirmed as disease-causing by referring clinical team

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

Last Updated: Oct 26, 2024

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