rs121918293
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Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate
The NM_017671.5(FERMT1):c.811C>T(p.Arg271*) variant causes a stop gained change. The variant allele was found at a frequency of 0.0000192 in 1,612,412 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: 𝑓 0.000059 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000015 ( 0 hom. )
Consequence
FERMT1
NM_017671.5 stop_gained
NM_017671.5 stop_gained
Scores
4
2
1
Clinical Significance
Conservation
PhyloP100: 5.40
Genes affected
FERMT1 (HGNC:15889): (FERM domain containing kindlin 1) This gene encodes a member of the fermitin family, and contains a FERM domain and a pleckstrin homology domain. The encoded protein is involved in integrin signaling and linkage of the actin cytoskeleton to the extracellular matrix. Mutations in this gene have been linked to Kindler syndrome. [provided by RefSeq, Dec 2009]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 12 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 20-6107570-G-A is Pathogenic according to our data. Variant chr20-6107570-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 2717.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr20-6107570-G-A is described in Lovd as [Pathogenic]. Variant chr20-6107570-G-A is described in Lovd as [Pathogenic].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FERMT1 | NM_017671.5 | c.811C>T | p.Arg271* | stop_gained | 6/15 | ENST00000217289.9 | NP_060141.3 | |
FERMT1 | XM_024451935.2 | c.811C>T | p.Arg271* | stop_gained | 6/15 | XP_024307703.1 | ||
FERMT1 | XM_047440259.1 | c.811C>T | p.Arg271* | stop_gained | 6/15 | XP_047296215.1 | ||
FERMT1 | XM_047440260.1 | c.526C>T | p.Arg176* | stop_gained | 5/14 | XP_047296216.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FERMT1 | ENST00000217289.9 | c.811C>T | p.Arg271* | stop_gained | 6/15 | 1 | NM_017671.5 | ENSP00000217289.4 |
Frequencies
GnomAD3 genomes AF: 0.0000591 AC: 9AN: 152158Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000318 AC: 8AN: 251240Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135800
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GnomAD4 exome AF: 0.0000151 AC: 22AN: 1460254Hom.: 0 Cov.: 29 AF XY: 0.0000151 AC XY: 11AN XY: 726488
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GnomAD4 genome AF: 0.0000591 AC: 9AN: 152158Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74326
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ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:5Other:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Kindler syndrome Pathogenic:3Other:1
not provided, no classification provided | literature only | GeneReviews | - | Common pathogenic variant - |
Pathogenic, no assertion criteria provided | literature only | OMIM | Jul 01, 2003 | - - |
Likely pathogenic, no assertion criteria provided | research | Institute of Human Genetics, University of Ulm | Jul 12, 2022 | - - |
Pathogenic, no assertion criteria provided | curation | Department Of Genetics, Sultan Qaboos University Hospital, Sultan Qaboos University | Dec 30, 2017 | - - |
FERMT1-related disorder Pathogenic:1
Pathogenic, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Dec 06, 2023 | The FERMT1 c.811C>T variant is predicted to result in premature protein termination (p.Arg271*). This variant has been reported in the homozygous or compound heterozygous state in many individuals with Kindler syndrome (see, for example: Siegel et al. 2003. PubMed ID: 12789646; Burch et al. 2006. PubMed ID: 16702500; Kantheti et al. 2017. PubMed ID: 27862150). This variant is reported in 0.012% of alleles in individuals of African descent in gnomAD. Nonsense variants in FERMT1 are expected to be pathogenic. This variant is interpreted as pathogenic. - |
not provided Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jul 13, 2023 | This sequence change creates a premature translational stop signal (p.Arg271*) in the FERMT1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in FERMT1 are known to be pathogenic (PMID: 14962093, 21936020). This variant is present in population databases (rs121918293, gnomAD 0.01%). This premature translational stop signal has been observed in individual(s) with Kindler syndrome (PMID: 12789646, 16702500, 27862150). ClinVar contains an entry for this variant (Variation ID: 2717). For these reasons, this variant has been classified as Pathogenic. - |
Computational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
CADD
Pathogenic
DANN
Uncertain
Eigen
Pathogenic
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
Vest4
GERP RS
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at