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NM_017946.4(FKBP14):c.362dup (p.Glu122fs) AND Ehlers-Danlos syndrome, kyphoscoliotic type, 2

Germline classification:
Pathogenic/Likely pathogenic (12 submissions)
Last evaluated:
Jan 27, 2024
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV000533832.25

Allele description

NM_017946.4(FKBP14):c.362dup (p.Glu122fs)

Genes:
FKBP14:FKBP prolyl isomerase 14 [Gene - OMIM - HGNC]
FKBP14-AS1:FKBP14 antisense RNA 1 [Gene - HGNC]
Variant type:
Duplication
Cytogenetic location:
7p14.3
Genomic location:
Preferred name:
NM_017946.4(FKBP14):c.362dup (p.Glu122fs)
Other names:
p.Glu122fs
HGVS:
  • NC_000007.14:g.30019115dup
  • NG_032173.1:g.12691dup
  • NM_017946.4:c.362dupMANE SELECT
  • NP_060416.1:p.Glu122fs
  • LRG_454t1:c.362dup
  • LRG_454:g.12691dup
  • NC_000007.13:g.30058726_30058727insG
  • NC_000007.13:g.30058731dup
  • NM_017946.2:c.362dupC
  • NM_017946.3:c.362dupC
  • NR_046478.2:n.648dup
  • NR_046479.2:n.404dup
  • p.Glu122Argfs*7
Protein change:
E122fs
Links:
OMIM: 614505.0001; dbSNP: rs542489955
NCBI 1000 Genomes Browser:
rs542489955
Molecular consequence:
  • NM_017946.4:c.362dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NR_046478.2:n.648dup - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_046479.2:n.404dup - non-coding transcript variant - [Sequence Ontology: SO:0001619]
Observations:
6

Condition(s)

Name:
Ehlers-Danlos syndrome, kyphoscoliotic type, 2
Synonyms:
Ehlers-Danlos syndrome with progressive kyphoscoliosis, myopathy, and hearing loss; Ehlers-Danlos syndrome, kyphoscoliotic and deafness type
Identifiers:
MONDO: MONDO:0013800; MedGen: C3281160; Orphanet: 300179; OMIM: 614557

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000045487OMIM
no assertion criteria provided
Pathogenic
(Feb 10, 2012)
germlineliterature only

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

SCV000652309Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Pathogenic
(Jan 27, 2024)
germlineclinical testing

PubMed (4)
[See all records that cite these PMIDs]

SCV000929975GeneReviews
no classification provided
not providedgermlineliterature only

PubMed (4)
[See all records that cite these PMIDs]

SCV001369762Centre for Mendelian Genomics, University Medical Centre Ljubljana
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely pathogenic
(Jan 20, 2020)
unknownclinical testing

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

SCV001429022Institute of Human Genetics, University of Leipzig Medical Center
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Jul 10, 2019)
germlineclinical testing

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

SCV001524457Baylor Genetics
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Mar 26, 2019)
paternalclinical testing

PubMed (5)
[See all records that cite these PMIDs]

SCV001593267Research Centre for Medical Genetics, Federal State Budgetary Scientific Institution
no assertion criteria provided
Pathogenic
(Oct 23, 2020)
germlineclinical testing

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

SCV002043791Equipe Genetique des Anomalies du Developpement, Université de Bourgogne
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenicbiparentalclinical testing

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

SCV002810392Fulgent Genetics, Fulgent Genetics
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Jul 22, 2021)
unknownclinical testing

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

SCV003822048Revvity Omics, Revvity
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Apr 30, 2022)
germlineclinical testing

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

SCV003924401Molecular Genetic Pathology Unit, University Of Rochester Medical Center
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(May 16, 2023)
germlineclinical testing

PubMed (5)
[See all records that cite these PMIDs]

SCV004099663Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)
Pathogenic
(Sep 8, 2023)
germlineclinical testing

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

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only
not providedbiparentalyesnot provided1not providednot providednot providedclinical testing
not providedgermlineyes2not providednot providednot providednot providedclinical testing
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing, literature only
not providedpaternalyesnot providednot providednot providednot providednot providedclinical testing
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing
Russiagermlinenot provided55not providednot providednot providedclinical 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

Ehlers-Danlos syndrome related to FKBP14 mutations: detailed cutaneous phenotype.

Bursztejn AC, Baumann M, Lipsker D.

Clin Exp Dermatol. 2017 Jan;42(1):64-67. doi: 10.1111/ced.12983. Epub 2016 Nov 30. Review.

PubMed [citation]
PMID:
27905128
See all PubMed Citations (10)

Details of each submission

From OMIM, SCV000045487.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (2)

Description

In 5 patients with Ehlers-Danlos syndrome with progressive kyphoscoliosis, myopathy, and hearing loss (EDSKSCL2; 614557) from 4 unrelated families of Austrian, Italian, French, and Turkish origin, Baumann et al. (2012) identified homozygosity for a 1-bp insertion within a 5C-nucleotide repeat in exon 3 (c.362dupC, NM_017946.2) of the FKBP14 gene, causing a frameshift predicted to result in a premature termination codon (Glu122ArgfsTer7). Western blot analysis demonstrated absence of FKBP14 in patient fibroblasts, and qRT-PCR analysis showed strongly reduced FKBP14 expression compared to controls, consistent with nonsense-mediated decay. In an unrelated patient with EDSKMH, Baumann et al. (2012) identified compound heterozygosity for the 362insC mutation and a 19-bp deletion (42_60del) in exon 1 of the FKBP14 gene (614505.0002), also predicted to result in a premature termination codon. The 362dupC mutation was linked to the same haplotype in all individuals, despite their geographically diverse origins, suggesting a possible founder event. Neither mutation was found in 200 controls of European descent.

In an 8-year-old Italian boy with EDSKSCL, Dordoni et al. (2016) identified compound heterozygosity for the recurrent c.362dupC mutation in exon 3 of the FKBP14 gene, and an in-frame 3-bp deletion (c.573_575del; 614505.0004) in exon 4, causing deletion of 1 residue (Glu191del). His unaffected parents were each heterozygous for 1 of the mutations.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot providednot providednot providednot providednot provided

From Invitae, SCV000652309.9

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (4)

Description

This sequence change creates a premature translational stop signal (p.Glu122Argfs*7) in the FKBP14 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in FKBP14 are known to be pathogenic (PMID: 22265013). This variant is present in population databases (rs542489955, gnomAD 0.1%), and has an allele count higher than expected for a pathogenic variant. This premature translational stop signal has been observed in individuals with Ehlers-Danlos syndrome (PMID: 22265013, 24677762, 27149304). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 279809). For these reasons, this variant has been classified as Pathogenic.

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

From GeneReviews, SCV000929975.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (4)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Centre for Mendelian Genomics, University Medical Centre Ljubljana, SCV001369762.2

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

Description

This variant was classified as: Likely pathogenic. The following ACMG criteria were applied in classifying this variant: PS1,PM2. This variant was detected in homozygous state.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providednot providednot providednot providednot providednot provided

From Institute of Human Genetics, University of Leipzig Medical Center, SCV001429022.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided1not providednot providednot provided

From Baylor Genetics, SCV001524457.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (5)

Description

This variant was determined to be pathogenic according to ACMG Guidelines, 2015 [PMID:25741868]. This variant has been previously reported in multiple affected families as disease-causing [PMID 22265013, 27905128, 28617417, 24677762]

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1paternalyesnot providednot providednot providednot providednot providednot providednot provided

From Research Centre for Medical Genetics, Federal State Budgetary Scientific Institution, SCV001593267.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1Russia5not providednot providedclinical testing PubMed (2)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot provided5not provided5not provided

From Equipe Genetique des Anomalies du Developpement, Université de Bourgogne, SCV002043791.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1biparentalyesnot providedBloodnot providednot providednot provided1not provided

From Fulgent Genetics, Fulgent Genetics, SCV002810392.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

From Revvity Omics, Revvity, SCV003822048.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Molecular Genetic Pathology Unit, University Of Rochester Medical Center, SCV003924401.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
11not providednot providedclinical testing PubMed (5)

Description

This variant was identified in the homozygous state in a patient with kyphoscoliotic Ehlers-Danlos Syndrome (kEDS). This frameshift variant causes a premature termination codon and is predicted to result in loss-of-function. This variant is a known pathogenic variant that has been reported multiple times in patients with kEDS, as either homozygous or compound heterozygous. This variant has been submitted to ClinVar as pathogenic over twenty times.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided1not providednot providednot provided

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV004099663.1

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

Description

Variant summary: FKBP14 c.362dupC (p.Glu122ArgfsX7) 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. The variant allele was found at a frequency of 0.00055 in 207878 control chromosomes. This frequency is not significantly higher than estimated for a pathogenic variant in FKBP14 causing Ehlers-Danlos Syndrome, Kyphoscoliotic And Deafness Type. c.362dupC has been reported in the literature in multiple individuals affected with Ehlers-Danlos Syndrome, Kyphoscoliotic And Deafness Type (e.g., Colman_2022). These data indicate that the variant is very likely to be associated with disease. The following publication has been ascertained in the context of this evaluation (PMID: 36054293). 20 submitters have cited clinical-significance assessments for this variant to ClinVar after 2014, and all submitters classified the variant as pathogenic/likely pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.

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

Last Updated: Jun 2, 2024