rs199469707
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Variant summary
Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1PM2PP5_Very_Strong
The NM_001044385.3(TMEM237):c.52C>T(p.Arg18Ter) variant causes a stop gained change. The variant allele was found at a frequency of 0.0000718 in 1,602,646 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 (★★).
Frequency
Genomes: 𝑓 0.000059 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000073 ( 0 hom. )
Consequence
TMEM237
NM_001044385.3 stop_gained
NM_001044385.3 stop_gained
Scores
4
2
1
Clinical Significance
Conservation
PhyloP100: 4.80
Genes affected
TMEM237 (HGNC:14432): (transmembrane protein 237) The protein encoded by this gene is a tetraspanin protein that is thought to be involved in WNT signaling. Defects in this gene are a cause of Joubert syndrome-14. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2012]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 18 ACMG points.
PVS1
?
Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant located near the start codon (<100nt), not predicted to undergo nonsense mediated mRNA decay. There are 25 pathogenic variants in the truncated region.
PM2
?
Very rare variant in population databases, with high coverage;
PP5
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Variant 2-201640915-G-A is Pathogenic according to our data. Variant chr2-201640915-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 31180.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-201640915-G-A is described in Lovd as [Pathogenic].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TMEM237 | NM_001044385.3 | c.52C>T | p.Arg18Ter | stop_gained | 2/13 | ENST00000409883.7 | |
TMEM237 | NM_152388.4 | c.28C>T | p.Arg10Ter | stop_gained | 2/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMEM237 | ENST00000409883.7 | c.52C>T | p.Arg18Ter | stop_gained | 2/13 | 5 | NM_001044385.3 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000592 AC: 9AN: 152010Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000607 AC: 15AN: 247028Hom.: 0 AF XY: 0.0000448 AC XY: 6AN XY: 133946
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ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:11
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Joubert syndrome 14 Pathogenic:6
Pathogenic, no assertion criteria provided | literature only | OMIM | Oct 05, 2012 | - - |
Pathogenic, criteria provided, single submitter | clinical testing | Invitae | Jul 23, 2022 | This sequence change creates a premature translational stop signal (p.Arg18*) in the TMEM237 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in TMEM237 are known to be pathogenic (PMID: 22152675). This variant is present in population databases (rs199469707, gnomAD 0.01%). This premature translational stop signal has been observed in individuals with Joubert syndrome (PMID: 22152675, 22981120). It is commonly reported in individuals of Hutterite ancestry (PMID: 22152675, 22981120). ClinVar contains an entry for this variant (Variation ID: 31180). For these reasons, this variant has been classified as Pathogenic. - |
Pathogenic, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Dec 29, 2021 | - - |
Pathogenic, criteria provided, single submitter | clinical testing | Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego | May 04, 2018 | This nonsense variant found in exon 2 of 13 is predicted to result in loss of normal protein function. This variant has been previously reported as a homozygous change in ten Canadian Hutterite patients with intellectual disability, a characteristic facial appearance, encephalocele, coloboma, renal disease, and additional features consistent with a diagnosis of a Joubert syndrome related disorder (PMID: 22152675, 17603801). The variant is present in the heterozygous state in the gnomAD population database at a frequency of 0.005% (15/275258) and thus is presumed to be rare. Based on the available evidence, c.52C>T (p.Arg18Ter) variant is classified as pathogenic. - |
Pathogenic, criteria provided, single submitter | clinical testing | Victorian Clinical Genetics Services, Murdoch Childrens Research Institute | Feb 02, 2022 | Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0102 - Loss of function is a known mechanism of disease in this gene and is associated with Joubert syndrome 14 (MIM#614424). (I) 0106 - This gene is associated with autosomal recessive disease. (I) 0201 - Variant is predicted to cause nonsense-mediated decay (NMD) and loss of protein (premature termination codon is located at least 54 nucleotides upstream of the final exon-exon junction). (SP) 0251 - This variant is heterozygous. (I) 0304 - Variant is present in gnomAD (v2) <0.01 for a recessive condition (16 heterozygotes, 0 homozygotes). (SP) 0701 - Other premature termination variants comparable to the one identified in this case have very strong previous evidence for pathogenicity. Many NMD-predicted variants in this gene have been reported as likely pathogenic/pathogenic (ClinVar). (SP) 0802 - This variant has moderate previous evidence of pathogenicity in unrelated individuals. It has been reported as homozygous in many related Hutterite individuals with severe Joubert syndrome related disorder (PMIDs: 17603801, 22152675). It has been described as a founder variant in Hutterite individuals (PMID: 31710777). It has also been reported as pathogenic in ClinVar, however ethnicity of those individuals were not provided. (SP) 1001 - This variant has strong functional evidence supporting abnormal protein function. Functional studies using patient fibroblast line showed defective ciliogenesis and pairing of centrioles, and reduced TMEM237 expression level (PMID: 22152675). (SP) 1205 - This variant has been shown to be maternally inherited. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign - |
Pathogenic, criteria provided, single submitter | clinical testing | Molecular Genetics, Royal Melbourne Hospital | Apr 22, 2022 | This sequence change creates a premature termination codon at position 18 in exon 2 (of 13) of TMEM237 ,p.(Arg18*). It is expected to result in an absent or disrupted protein product, and loss of function is the established mechanism of disease for this gene (PMID: 22152675). The variant is present in a large population cohort at a frequency of 0.006%, which is consistent with a recessive condition (rs199469707, 16/278,360 alleles, 0 homozygotes in gnomAD v2.1). The variant has been identified in individuals with Joubert syndrome, and segregates with the condition in the homozygous state in multiple related Canadian Hutterite families. Fibroblast cell lines from homozygous cases show loss of TMEM237 expression, and defective ciliogenesis and pairing of centrioles (PMID: 22152675). Based on the classification scheme RMH Modified ACMG Guidelines v1.4.0, this variant is classified as PATHOGENIC. Following criteria are met: PVS1, PP1_Strong, PM2_Supporting, PP4. - |
not provided Pathogenic:3
Pathogenic, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | - | - - |
Pathogenic, no assertion criteria provided | clinical testing | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ | - | - - |
Pathogenic, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Joubert syndrome and related disorders Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | May 06, 2022 | Variant summary: TMEM237 c.52C>T (p.Arg18X) 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. Truncations downstream of this position have been classified as pathogenic within ClinVar. The variant allele was found at a frequency of 6.1e-05 in 247028 control chromosomes (gnomAD). This frequency is not significantly higher than expected for a pathogenic variant in TMEM237 causing Joubert Syndrome And Related Disorders (6.1e-05 vs 0.0004), allowing no conclusion about variant significance. The variant was found at an 8% carrier frequency rate within the Hutterite communities of Canada and the Northern United States, indicating a founder effect for the variant. Subsequently, c.52C>T has been reported in the literature in multiple homozygous individuals affected with Joubert Syndrome And Related Disorders from Hutterite communities (Huang_2011). The variant was also found in at least one compound heterozygous, presumably non-Hutterite individual (Clark_2019). These data indicate that the variant is very likely to be associated with disease. Huang_2011 has shown that fibroblasts homozygous for the variant have defects in ciliogenesis with no detectable ciliated cells as seen via microscopy. Huang_2011 also showed that the variant causes large reductions (98%) in TMEM237 transcripts and fibroblasts with the variant had dysregulated Wnt signaling. Three ClinVar submitters have assessed the variant since 2014: all three classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. - |
Familial aplasia of the vermis Pathogenic:1
Pathogenic, no assertion criteria provided | curation | GeneReviews | Mar 29, 2012 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
CADD
Pathogenic
DANN
Uncertain
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Uncertain
D
MutationTaster
Benign
A;A
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