NM_001079802.2(FKTN):c.489C>G (p.Ile163Met) AND Walker-Warburg congenital muscular dystrophy

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Sep 27, 2017
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:: RCV000634054.7

Allele description [Variation Report for NM_001079802.2(FKTN):c.489C>G (p.Ile163Met)]

NM_001079802.2(FKTN):c.489C>G (p.Ile163Met)

Gene:

FKTN:fukutin [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

9q31.2

Genomic location:

Preferred name:

NM_001079802.2(FKTN):c.489C>G (p.Ile163Met)

HGVS:

NC_000009.12:g.105604334C>G
NG_008754.1:g.51205C>G
NM_001079802.2:c.489C>GMANE SELECT
NM_001198963.2:c.489C>G
NM_001351496.2:c.489C>G
NM_001351497.2:c.420C>G
NM_001351498.2:c.489C>G
NM_001351499.2:c.93C>G
NM_001351500.2:c.93C>G
NM_001351501.2:c.93C>G
NM_001351502.2:c.93C>G
NM_006731.2:c.489C>G
NP_001073270.1:p.Ile163Met
NP_001073270.1:p.Ile163Met
NP_001185892.1:p.Ile163Met
NP_001338425.1:p.Ile163Met
NP_001338426.1:p.Ile140Met
NP_001338427.1:p.Ile163Met
NP_001338428.1:p.Ile31Met
NP_001338429.1:p.Ile31Met
NP_001338430.1:p.Ile31Met
NP_001338431.1:p.Ile31Met
NP_006722.2:p.Ile163Met
LRG_434t1:c.489C>G
LRG_434t2:c.489C>G
LRG_434:g.51205C>G
LRG_434p1:p.Ile163Met
LRG_434p2:p.Ile163Met
NC_000009.11:g.108366615C>G
NM_001079802.1:c.489C>G
NR_147213.2:n.704C>G
NR_147214.2:n.612C>G

Protein change:

I140M

Links:

dbSNP: rs980208971

NCBI 1000 Genomes Browser:

rs980208971

Molecular consequence:

NM_001079802.2:c.489C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001198963.2:c.489C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001351496.2:c.489C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001351497.2:c.420C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001351498.2:c.489C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001351499.2:c.93C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001351500.2:c.93C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001351501.2:c.93C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001351502.2:c.93C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_006731.2:c.489C>G - missense variant - [Sequence Ontology: SO:0001583]
NR_147213.2:n.704C>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_147214.2:n.612C>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Walker-Warburg congenital muscular dystrophy
Synonyms:: Muscular dystrophy-dystroglycanopathy, type A; Walker-Warburg syndrome
Identifiers:: MONDO: MONDO:0000171; MedGen: C0265221; Orphanet: 899; OMIM: PS236670

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000755332	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Sep 27, 2017)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000755332

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Sep 27, 2017)

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

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000755332.4

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

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0"). This variant has not been reported in the literature in individuals with FKTN-related disease. This variant is not present in population databases (ExAC no frequency). This sequence change replaces isoleucine with methionine at codon 163 of the FKTN protein (p.Ile163Met). The isoleucine residue is weakly conserved and there is a small physicochemical difference between isoleucine and methionine.

#	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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