NM_001079802.2(FKTN):c.411C>A (p.Cys137Ter) AND Walker-Warburg congenital muscular dystrophy

Clinical significance:Pathogenic (Last evaluated: Oct 9, 2020)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:

Allele description [Variation Report for NM_001079802.2(FKTN):c.411C>A (p.Cys137Ter)]

NM_001079802.2(FKTN):c.411C>A (p.Cys137Ter)

FKTN:fukutin [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Genomic location:
Preferred name:
NM_001079802.2(FKTN):c.411C>A (p.Cys137Ter)
  • NC_000009.12:g.105604256C>A
  • NG_008754.1:g.51127C>A
  • NM_001079802.1:c.411C>A
  • NM_001079802.2:c.411C>AMANE SELECT
  • NM_001198963.2:c.411C>A
  • NM_001351496.2:c.411C>A
  • NM_001351497.2:c.342C>A
  • NM_001351498.2:c.411C>A
  • NM_001351499.2:c.15C>A
  • NM_001351500.2:c.15C>A
  • NM_001351501.2:c.15C>A
  • NM_001351502.2:c.15C>A
  • NM_006731.2:c.411C>A
  • NP_001073270.1:p.Cys137Ter
  • NP_001073270.1:p.Cys137Ter
  • NP_001185892.1:p.Cys137Ter
  • NP_001338425.1:p.Cys137Ter
  • NP_001338426.1:p.Cys114Ter
  • NP_001338427.1:p.Cys137Ter
  • NP_001338428.1:p.Cys5Ter
  • NP_001338429.1:p.Cys5Ter
  • NP_001338430.1:p.Cys5Ter
  • NP_001338431.1:p.Cys5Ter
  • NP_006722.2:p.Cys137Ter
  • LRG_434t1:c.411C>A
  • LRG_434t2:c.411C>A
  • LRG_434:g.51127C>A
  • LRG_434p1:p.Cys137Ter
  • LRG_434p2:p.Cys137Ter
  • NC_000009.11:g.108366537C>A
  • NP_001073270.1:p.Cys137*
  • NR_147213.2:n.626C>A
  • NR_147214.2:n.534C>A
Protein change:
dbSNP: rs537001725
NCBI 1000 Genomes Browser:
Molecular consequence:
  • NR_147213.2:n.626C>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_147214.2:n.534C>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_001079802.1:c.411C>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001079802.2:c.411C>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001198963.2:c.411C>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001351496.2:c.411C>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001351497.2:c.342C>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001351498.2:c.411C>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001351499.2:c.15C>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001351500.2:c.15C>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001351501.2:c.15C>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001351502.2:c.15C>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_006731.2:c.411C>A - nonsense - [Sequence Ontology: SO:0001587]


Walker-Warburg congenital muscular dystrophy (MDDGA1)
HARD syndrome; Muscular dystrophy-dystroglycanopathy, type A; Walker-Warburg syndrome
MONDO: MONDO:0000171; MedGen: C0265221; Orphanet: 899; OMIM: PS236670

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
SCV001233310Invitaecriteria provided, single submitter
(Oct 9, 2020)
germlineclinical testing

PubMed (6)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing



Clinical genomics can facilitate countrywide estimation of autosomal recessive disease burden.

Abouelhoda M, Sobahy T, El-Kalioby M, Patel N, Shamseldin H, Monies D, Al-Tassan N, Ramzan K, Imtiaz F, Shaheen R, Alkuraya FS.

Genet Med. 2016 Dec;18(12):1244-1249. doi: 10.1038/gim.2016.37. Epub 2016 Apr 28.

PubMed [citation]

Congenital muscular dystrophies in the UK population: Clinical and molecular spectrum of a large cohort diagnosed over a 12-year period.

Sframeli M, Sarkozy A, Bertoli M, Astrea G, Hudson J, Scoto M, Mein R, Yau M, Phadke R, Feng L, Sewry C, Fen ANS, Longman C, McCullagh G, Straub V, Robb S, Manzur A, Bushby K, Muntoni F.

Neuromuscul Disord. 2017 Sep;27(9):793-803. doi: 10.1016/j.nmd.2017.06.008. Epub 2017 Jun 16.

PubMed [citation]
See all PubMed Citations (6)

Details of each submission

From Invitae, SCV001233310.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (6)


This sequence change creates a premature translational stop signal (p.Cys137*) in the FKTN gene. It is expected to result in an absent or disrupted protein product. This variant is present in population databases (rs537001725, ExAC 0.03%). This variant has been observed in individuals affected with clinical features FKTN-related disease (PMID: 27124789, 28688748). ClinVar contains an entry for this variant (Variation ID: 167069). Loss-of-function variants in FKTN are known to be pathogenic (PMID: 17044012, 17878207, 18752264). For these reasons, this variant has been classified as Pathogenic.

OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: May 10, 2021

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