NM_001136193.2(FASTKD2):c.319_323del (p.Leu107fs) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jan 7, 2024
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:: RCV003829340.2

Allele description [Variation Report for NM_001136193.2(FASTKD2):c.319_323del (p.Leu107fs)]

NM_001136193.2(FASTKD2):c.319_323del (p.Leu107fs)

Gene:

FASTKD2:FAST kinase domains 2 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

2q33.3

Genomic location:

Preferred name:

NM_001136193.2(FASTKD2):c.319_323del (p.Leu107fs)

HGVS:

NC_000002.12:g.206767012_206767016del
NG_008984.1:g.6625_6629del
NM_001136193.2:c.319_323delMANE SELECT
NM_001136194.2:c.319_323del
NM_014929.4:c.319_323del
NP_001129665.1:p.Leu107fs
NP_001129666.1:p.Leu107fs
NP_055744.2:p.Leu107fs
NC_000002.11:g.207631734_207631738del
NC_000002.11:g.207631736_207631740del

Protein change:

L107fs

Molecular consequence:

NM_001136193.2:c.319_323del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001136194.2:c.319_323del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_014929.4:c.319_323del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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MULTISPECIES: redoxin domain-containing protein [unclassified Methylocaldum]
MULTISPECIES: redoxin domain-containing protein [unclassified Methylocaldum]
gi|1830360834|ref|WP_168175475.1|

Protein
Homo sapiens elongation factor G2 (EFG2) mRNA, complete cds; nuclear gene for mi...
Homo sapiens elongation factor G2 (EFG2) mRNA, complete cds; nuclear gene for mitochondrial product
gi|14039830|gb|AF367997.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004627261	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jan 7, 2024)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 18771761, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004627261

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jan 7, 2024)

germline

clinical testing

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

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

FASTKD2 nonsense mutation in an infantile mitochondrial encephalomyopathy associated with cytochrome c oxidase deficiency.

Ghezzi D, Saada A, D'Adamo P, Fernandez-Vizarra E, Gasparini P, Tiranti V, Elpeleg O, Zeviani M.

Am J Hum Genet. 2008 Sep;83(3):415-23. doi: 10.1016/j.ajhg.2008.08.009. Epub 2008 Sep 4.

PubMed [citation]

PMID:: 18771761
PMCID:: PMC2556431

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, SCV004627261.1

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

Description

This sequence change creates a premature translational stop signal (p.Leu107Cysfs*2) in the FASTKD2 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in FASTKD2 are known to be pathogenic (PMID: 18771761). This variant is present in population databases (rs763480439, gnomAD 0.005%). This variant has not been reported in the literature in individuals affected with FASTKD2-related conditions. For these reasons, this variant has been 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

Last Updated: Sep 29, 2024

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