NM_001079802.2(FKTN):c.488T>A (p.Ile163Asn) AND Walker-Warburg congenital muscular dystrophy

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Aug 28, 2021
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:: RCV001225108.8

Allele description [Variation Report for NM_001079802.2(FKTN):c.488T>A (p.Ile163Asn)]

NM_001079802.2(FKTN):c.488T>A (p.Ile163Asn)

Gene:

FKTN:fukutin [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

9q31.2

Genomic location:

Preferred name:

NM_001079802.2(FKTN):c.488T>A (p.Ile163Asn)

HGVS:

NC_000009.12:g.105604333T>A
NG_008754.1:g.51204T>A
NM_001079802.2:c.488T>AMANE SELECT
NM_001198963.2:c.488T>A
NM_001351496.2:c.488T>A
NM_001351497.2:c.419T>A
NM_001351498.2:c.488T>A
NM_001351499.2:c.92T>A
NM_001351500.2:c.92T>A
NM_001351501.2:c.92T>A
NM_001351502.2:c.92T>A
NM_006731.2:c.488T>A
NP_001073270.1:p.Ile163Asn
NP_001185892.1:p.Ile163Asn
NP_001338425.1:p.Ile163Asn
NP_001338426.1:p.Ile140Asn
NP_001338427.1:p.Ile163Asn
NP_001338428.1:p.Ile31Asn
NP_001338429.1:p.Ile31Asn
NP_001338430.1:p.Ile31Asn
NP_001338431.1:p.Ile31Asn
NP_006722.2:p.Ile163Asn
LRG_434t1:c.488T>A
LRG_434t2:c.488T>A
LRG_434:g.51204T>A
LRG_434p2:p.Ile163Asn
NC_000009.11:g.108366614T>A
NM_001079802.1:c.488T>A
NR_147213.2:n.703T>A
NR_147214.2:n.611T>A

Protein change:

I140N

Links:

dbSNP: rs1828461999

NCBI 1000 Genomes Browser:

rs1828461999

Molecular consequence:

NM_001079802.2:c.488T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001198963.2:c.488T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001351496.2:c.488T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001351497.2:c.419T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001351498.2:c.488T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001351499.2:c.92T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001351500.2:c.92T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001351501.2:c.92T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001351502.2:c.92T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_006731.2:c.488T>A - missense variant - [Sequence Ontology: SO:0001583]
NR_147213.2:n.703T>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_147214.2:n.611T>A - 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
SCV001397344	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Aug 28, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002079576	Natera, Inc.	no assertion criteria provided	Uncertain significance (Jun 18, 2021)	germline	clinical testing

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001397344

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Aug 28, 2021)

germline

clinical testing

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

SCV002079576

Natera, Inc.

no assertion criteria provided

Uncertain significance
(Jun 18, 2021)

germline

clinical testing

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, SCV001397344.4

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

Description

This sequence change replaces isoleucine with asparagine at codon 163 of the FKTN protein (p.Ile163Asn). The isoleucine residue is weakly conserved and there is a large physicochemical difference between isoleucine and asparagine. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals affected with FKTN-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C35"). 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.

#	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 Natera, Inc., SCV002079576.1

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

#	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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