NM_001079802.2(FKTN):c.607C>T (p.Arg203Ter) AND Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 4

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Mar 21, 2017
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:: RCV000590733.1

Allele description [Variation Report for NM_001079802.2(FKTN):c.607C>T (p.Arg203Ter)]

NM_001079802.2(FKTN):c.607C>T (p.Arg203Ter)

Gene:

FKTN:fukutin [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

9q31.2

Genomic location:

Preferred name:

NM_001079802.2(FKTN):c.607C>T (p.Arg203Ter)

HGVS:

NC_000009.12:g.105604452C>T
NG_008754.1:g.51323C>T
NM_001079802.2:c.607C>TMANE SELECT
NM_001198963.2:c.607C>T
NM_001351496.2:c.607C>T
NM_001351497.2:c.538C>T
NM_001351498.2:c.607C>T
NM_001351499.2:c.211C>T
NM_001351500.2:c.211C>T
NM_001351501.2:c.211C>T
NM_001351502.2:c.211C>T
NM_006731.2:c.607C>T
NP_001073270.1:p.Arg203Ter
NP_001073270.1:p.Arg203Ter
NP_001185892.1:p.Arg203Ter
NP_001338425.1:p.Arg203Ter
NP_001338426.1:p.Arg180Ter
NP_001338427.1:p.Arg203Ter
NP_001338428.1:p.Arg71Ter
NP_001338429.1:p.Arg71Ter
NP_001338430.1:p.Arg71Ter
NP_001338431.1:p.Arg71Ter
NP_006722.2:p.Arg203Ter
LRG_434t1:c.607C>T
LRG_434t2:c.607C>T
LRG_434:g.51323C>T
LRG_434p1:p.Arg203Ter
LRG_434p2:p.Arg203Ter
NC_000009.11:g.108366733C>T
NM_001079802.1:c.607C>T
NM_001079802.2:c.607C>T
NM_001351497.1:c.538C>T
NR_147213.2:n.822C>T
NR_147214.2:n.730C>T

Protein change:

R180*

Links:

dbSNP: rs746763506

NCBI 1000 Genomes Browser:

rs746763506

Molecular consequence:

NR_147213.2:n.822C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_147214.2:n.730C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_001079802.2:c.607C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001198963.2:c.607C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001351496.2:c.607C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001351497.2:c.538C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001351498.2:c.607C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001351499.2:c.211C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001351500.2:c.211C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001351501.2:c.211C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001351502.2:c.211C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_006731.2:c.607C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:: Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 4 (MDDGA4)
Synonyms:: Fukuyama type muscular dystrophy; Muscular dystrophy, congenital progressive, with mental retardation; Muscular dystrophy, congenital, with central nervous system involvement; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0009678; MedGen: C0410174; Orphanet: 588; Orphanet: 899; OMIM: 253800

Recent activity

Clear Turn Off Turn On

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
SCV000698717	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Pathogenic (May 6, 2016)	germline	clinical testing	PubMed (1) [See all records that cite this PMID] LabCorp Variant Classification Summary - May 2015.docx, Citation Link,
SCV000790450	Counsyl	criteria provided, single submitter (Counsyl Autosomal Recessive and X-Linked Classification Criteria (2018))	Pathogenic (Mar 21, 2017)	unknown	clinical testing	PubMed (2) [See all records that cite these PMIDs] 11165248, 26809617 Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000698717

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Pathogenic
(May 6, 2016)

germline

clinical testing

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

LabCorp Variant Classification Summary - May 2015.docx,

Citation Link,

SCV000790450

Counsyl

criteria provided, single submitter

(Counsyl Autosomal Recessive and X-Linked Classification Criteria (2018))

Pathogenic
(Mar 21, 2017)

unknown

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

Citation Link

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
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Structural organization, complete genomic sequences and mutational analyses of the Fukuyama-type congenital muscular dystrophy gene, fukutin.

Kobayashi K, Sasaki J, Kondo-Iida E, Fukuda Y, Kinoshita M, Sunada Y, Nakamura Y, Toda T.

FEBS Lett. 2001 Feb 2;489(2-3):192-6.

PubMed [citation]

PMID:: 11165248

Diagnosis of late-onset Pompe disease and other muscle disorders by next-generation sequencing.

Lévesque S, Auray-Blais C, Gravel E, Boutin M, Dempsey-Nunez L, Jacques PE, Chenier S, Larue S, Rioux MF, Al-Hertani W, Nadeau A, Mathieu J, Maranda B, Désilets V, Waters PJ, Keutzer J, Austin S, Kishnani P.

Orphanet J Rare Dis. 2016 Jan 25;11:8. doi: 10.1186/s13023-016-0390-6.

PubMed [citation]

PMID:: 26809617
PMCID:: PMC4727295

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000698717.1

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

Description

Variant summary: The FKTN variant, c.607C>T (p.Arg203X) causes a nonsense mutation in exon 5 resulting in a premature termination codon, a known mechanism for disease, as these types of variants are predicted to cause transcript degradation through nonsense mediated decay or produce a truncated protein. The varinat of interest was observed in the large, broad control population, ExAC, with an allele frequency of 1/121290, which does not exceed the estimated maximum expected allele frequency for a pathogenic FKTN variant of 1/200 for Fukuyama Congenital Muscular Dystrophy. The variant of interest has been reported in multiple affected individuals dx with Fukuyama Congenital Muscular Dystrophy (patient was homozygous for variant) and Muscular dystrophy-dystroglycanopathy(limb-girdle) via publications. One reputable database cites the variant as disease-causing. Therefore, taking all available lines of evidence into consideration, the variant of interest is 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

From Counsyl, SCV000790450.1

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

#	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

Last Updated: Oct 8, 2024

ClinVar

Relating variation to medicine