NM_001079802.2(FKTN):c.567_568delinsTT (p.Leu189_Arg190delinsPheTer) AND Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 4

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Nov 7, 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:: RCV002469392.1

Allele description [Variation Report for NM_001079802.2(FKTN):c.567_568delinsTT (p.Leu189_Arg190delinsPheTer)]

NM_001079802.2(FKTN):c.567_568delinsTT (p.Leu189_Arg190delinsPheTer)

Gene:

FKTN:fukutin [Gene - OMIM - HGNC]

Variant type:

Indel

Cytogenetic location:

9q31.2

Genomic location:

Preferred name:

NM_001079802.2(FKTN):c.567_568delinsTT (p.Leu189_Arg190delinsPheTer)

HGVS:

NC_000009.12:g.105604412_105604413delinsTT
NG_008754.1:g.51283_51284delinsTT
NM_001079802.2:c.567_568delinsTTMANE SELECT
NM_001198963.2:c.567_568delinsTT
NM_001351496.2:c.567_568delinsTT
NM_001351497.2:c.498_499delinsTT
NM_001351498.2:c.567_568delinsTT
NM_001351499.2:c.171_172delinsTT
NM_001351500.2:c.171_172delinsTT
NM_001351501.2:c.171_172delinsTT
NM_001351502.2:c.171_172delinsTT
NM_006731.2:c.567_568delinsTT
NP_001073270.1:p.Leu189_Arg190delinsPheTer
NP_001185892.1:p.Leu189_Arg190delinsPheTer
NP_001338425.1:p.Leu189_Arg190delinsPheTer
NP_001338426.1:p.Leu166_Arg167delinsPheTer
NP_001338427.1:p.Leu189_Arg190delinsPheTer
NP_001338428.1:p.Leu57_Arg58delinsPheTer
NP_001338429.1:p.Leu57_Arg58delinsPheTer
NP_001338430.1:p.Leu57_Arg58delinsPheTer
NP_001338431.1:p.Leu57_Arg58delinsPheTer
NP_006722.2:p.Leu189_Arg190delinsPheTer
LRG_434t2:c.567_568delinsTT
LRG_434:g.51283_51284delinsTT
LRG_434p2:p.Leu189_Arg190delinsPheTer
NC_000009.11:g.108366693_108366694delinsTT
NR_147213.2:n.782_783delinsTT
NR_147214.2:n.690_691delinsTT

Links:

dbSNP: rs2132800044

NCBI 1000 Genomes Browser:

rs2132800044

Molecular consequence:

NR_147213.2:n.782_783delinsTT - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_147214.2:n.690_691delinsTT - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_001079802.2:c.567_568delinsTT - nonsense - [Sequence Ontology: SO:0001587]
NM_001198963.2:c.567_568delinsTT - nonsense - [Sequence Ontology: SO:0001587]
NM_001351496.2:c.567_568delinsTT - nonsense - [Sequence Ontology: SO:0001587]
NM_001351497.2:c.498_499delinsTT - nonsense - [Sequence Ontology: SO:0001587]
NM_001351498.2:c.567_568delinsTT - nonsense - [Sequence Ontology: SO:0001587]
NM_001351499.2:c.171_172delinsTT - nonsense - [Sequence Ontology: SO:0001587]
NM_001351500.2:c.171_172delinsTT - nonsense - [Sequence Ontology: SO:0001587]
NM_001351501.2:c.171_172delinsTT - nonsense - [Sequence Ontology: SO:0001587]
NM_001351502.2:c.171_172delinsTT - nonsense - [Sequence Ontology: SO:0001587]
NM_006731.2:c.567_568delinsTT - 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

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002766328	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Likely pathogenic (Nov 7, 2022)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002766328

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

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Likely pathogenic
(Nov 7, 2022)

germline

clinical testing

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

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV002766328.1

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

Description

Variant summary: FKTN c.567_568delinsTT (p.Leu189PhefsX2) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. Truncations downstream of this position have been classified as pathogenic by our laboratory. The frequency of this variant in the general population could not be determined as the technology used for large population databases (ExAC, gnomAD, ESP, 1000G) cannot detect variants of this type. To our knowledge, no occurrence of c.567_568delinsTT in individuals affected with Walker-Warburg Syndrome and no experimental evidence demonstrating its impact on protein function have been reported. A ClinVar submitter (evaluation after 2014) cites the variant as pathogenic. Based on the evidence outlined above, the variant was classified as likely 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: Oct 8, 2024

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