Genetic Variant FKBP10:p.Gly278ArgfsTer95 (chr17-41819306-T-TC) – ACMG Classification: Pathogenic (18 pts)

Variant summary

Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1PM2PP5_Very_Strong

The NM_021939.4(FKBP10):c.831dupC(p.Gly278ArgfsTer95) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000967 in 1,613,250 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (★★). Variant results in nonsense mediated mRNA decay.

Frequency

Genomes: 𝑓 0.00015 ( 0 hom., cov: 31)

Exomes 𝑓: 0.000091 ( 0 hom. )

Consequence

FKBP10
NM_021939.4 frameshift

Scores

Not classified

Clinical Significance

Pathogenic criteria provided, multiple submitters, no conflicts P:19U:1

Conservation

PhyloP100: -0.727

Variant links:

Genes affected

FKBP10 (HGNC:18169): (FKBP prolyl isomerase 10) The protein encoded by this gene belongs to the FKBP-type peptidyl-prolyl cis/trans isomerase (PPIase) family. This protein localizes to the endoplasmic reticulum and acts as a molecular chaperone. Alternatively spliced variants encoding different isoforms have been reported, but their biological validity has not been determined.[provided by RefSeq, Nov 2009]

FKBP10 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Pathogenic. Variant got 18 ACMG points.

PVS1

Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.

PM2

Very rare variant in population databases, with high coverage;

PP5

Variant 17-41819306-T-TC is Pathogenic according to our data. Variant chr17-41819306-T-TC is described in ClinVar as [Pathogenic]. Clinvar id is 438659.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FKBP10	NM_021939.4 link	c.831dupC	p.Gly278ArgfsTer95	frameshift_variant	Exon 5 of 10	ENST00000321562.9	NP_068758.3	Q96AY3-1A0A024R1W3Q8NAG5Q658U4
FKBP10	XM_011525099.4 link	c.831dupC	p.Gly278ArgfsTer95	frameshift_variant	Exon 5 of 11		XP_011523401.1
FKBP10	XM_011525100.3 link	c.558dupC	p.Gly187ArgfsTer95	frameshift_variant	Exon 4 of 10		XP_011523402.1
FKBP10	XM_047436515.1 link	c.558dupC	p.Gly187ArgfsTer95	frameshift_variant	Exon 4 of 9		XP_047292471.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FKBP10	ENST00000321562.9 link	c.831dupC	p.Gly278ArgfsTer95	frameshift_variant	Exon 5 of 10	1	NM_021939.4	ENSP00000317232.4		Q96AY3-1

Frequencies

GnomAD3 genomes

AF:

0.000152

AC:

AN:

151466

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000364

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000390

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.0000952

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000589

Gnomad OTH

AF:

0.000479

GnomAD3 exomes

AF:

0.000108

AC:

AN:

250308

Hom.:

AF XY:

0.0000811

AC XY:

AN XY:

135638

show subpopulations

Gnomad AFR exome

AF:

0.000498

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.0000544

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.000370

Gnomad NFE exome

AF:

0.0000797

Gnomad OTH exome

AF:

0.000164

GnomAD4 exome

AF:

0.0000910

AC:

133

AN:

1461670

Hom.:

Cov.:

AF XY:

0.0000921

AC XY:

AN XY:

727122

show subpopulations

Gnomad4 AFR exome

AF:

0.000627

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.000115

Gnomad4 EAS exome

AF:

0.0000756

Gnomad4 SAS exome

AF:

0.0000464

Gnomad4 FIN exome

AF:

0.000244

Gnomad4 NFE exome

AF:

0.0000719

Gnomad4 OTH exome

AF:

0.000149

GnomAD4 genome

AF:

0.000152

AC:

AN:

151580

Hom.:

Cov.:

AF XY:

0.000122

AC XY:

AN XY:

74042

show subpopulations

Gnomad4 AFR

AF:

0.000363

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.000390

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.0000952

Gnomad4 NFE

AF:

0.0000589

Gnomad4 OTH

AF:

0.000474

Bravo

AF:

0.000132

EpiCase

AF:

0.000109

EpiControl

AF:

0.000119

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:19Uncertain:1

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Osteogenesis imperfecta type 11

Pathogenic:8Uncertain:1

3billion

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The variant is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.011%). The variant is predicted to result in a loss or disruption of normal protein function through nonsense-mediated decay (NMD) or protein truncation. Multiple pathogenic variants are reported downstream of the variant. The variant has been reported at least twice as pathogenic with clinical assertions and evidence for the classification (ClinVar ID: VCV000438659 / PMID: 20362275 / 3billion dataset). Therefore, this variant is classified as Pathogenic according to the recommendation of ACMG/AMP guideline. -

Jul 10, 2024

Dr.Nikuei Genetic Center

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

May 28, 2019

Mendelics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Apr 20, 2017

Bioscientia Institut fuer Medizinische Diagnostik GmbH, Sonic Healthcare

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Mar 13, 2023

Department of Pathology and Laboratory Medicine, Sinai Health System

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: research

- -

Suma Genomics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Apr 23, 2021

Illumina Laboratory Services, Illumina

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The FKBP10 c.831dupC (p.Gly278ArgfsTer95) variant results in a frameshift and is predicted to result in premature termination or absence of the protein. In a selection of the literature, the p.Gly278ArgfsTer95 variant has been reported in a homozygous state in at least five affected individuals from three unrelated families (Alanay et al. 2010; Shaheen et al. 2011; Kelly et al. 2011), in a compound heterozygous state with another frameshift variant in two affected individuals from one family (Schwarze et al. 2011), and in a compound heterozygous state with a missense variant in two unrelated individuals (Vorster et al. 2017). The affected individuals presented with osteogenesis imperfecta with or without a range of additional phenotypes. In addition, in one study of 91 individuals with non-syndromic osteogenesis imperfecta type 3, the p.Gly278ArgfsTer95 variant was found in a homozygous state in 35/91 (38%) affected individuals who shared the same haplotype (Vorster et al. 2017). In studies on mRNA isolated from patient cells, the p.Gly278ArgfsTer95 was shown to affect mRNA stability resulting in no measurable stable mRNA and absence of protein on Western blotting (Schwarze et al. 2013). The p.Gly278ArgfsTer95 variant was absent from at least 210 ethnically matched control alleles and is found at a frequency of 0.000445 in the African American population of the Genome Aggregation Database. Based on the collective evidence and application of the ACMG criteria, the c.831dupC (p.Gly278ArgfsTer95) variant is classified as pathogenic for osteogenesis imperfecta with or without joint contractures. -

Apr 01, 2023

Clinical Laboratory Sciences Program (CLSP), King Saud bin Abdulaziz University for Health Sciences (KSAU-HS)

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Mar 29, 2024

Genomic Medicine Center of Excellence, King Faisal Specialist Hospital and Research Centre

Significance: Uncertain significance

Review Status: flagged submission

Collection Method: clinical testing

- -

not provided

Pathogenic:6

Mar 31, 2017

Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Nov 19, 2018

Center for Personalized Medicine, Children's Hospital Los Angeles

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Mar 02, 2025

GeneDx

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss of function is a known mechanism of disease; This variant is associated with the following publications: (PMID: 20362275, 31001443, 27509835, 29499418, 28492130, 31429852, 31589614, 37644014, 38178268, 36703223, 37270749, 36655627, 34902613, 32123938, 30755392, 20839288, 29635034, 34173012, 25931047, 26538303, 30993005, 28378777, 28116328, 29158687, 27146342, 23443412, 21670757, 21567934, 22107750, 29620724, 27762305, 27717089, 28346524, 28177155, 22718341, 34743040, 38374194) -

Nov 30, 2019

Blueprint Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jan 10, 2022

Revvity Omics, Revvity

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Oct 02, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change creates a premature translational stop signal (p.Gly278Argfs*95) in the FKBP10 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in FKBP10 are known to be pathogenic (PMID: 22689593, 22949511). This variant is present in population databases (rs781896189, gnomAD 0.04%). This premature translational stop signal has been observed in individuals with autosomal recessive osteogenesis imperfecta (PMID: 20362275, 26538303, 27509835, 27717089, 27762305). ClinVar contains an entry for this variant (Variation ID: 438659). For these reasons, this variant has been classified as Pathogenic. -

Osteogenesis imperfecta

Pathogenic:1

Oct 04, 2024

Al Jalila Children’s Genomics Center, Al Jalila Childrens Speciality Hospital

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: research

PVS1, PM3_VeryStrong, PM2 -

Abnormality of the skeletal system

Pathogenic:1

Jul 10, 2021

Kariminejad - Najmabadi Pathology & Genetics Center

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Bruck syndrome 1

Pathogenic:1

Jun 01, 2011

OMIM

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

- -

Osteogenesis imperfecta type 12

Pathogenic:1

Jun 01, 2011

OMIM

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

- -

Bruck syndrome 1;C3151218:Osteogenesis imperfecta type 11

Pathogenic:1

Apr 15, 2024

Fulgent Genetics, Fulgent Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

17-41819306-TC-TCC

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over