chr2-201640915-G-A

Position:

chr2-201640915-G-A

Variant summary

Our verdict is Pathogenic. Variant got 14 ACMG points: 14P and 0B. PVS1_StrongPM2PP5_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

Scores

Clinical Significance

Pathogenic criteria provided, multiple submitters, no conflicts P:12

Conservation

PhyloP100: 4.80

Variant links:

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]

TMEM237 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Pathogenic. Variant got 14 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. Fraction of 0.958 CDS is truncated, and there are 3 pathogenic variants in the truncated region.

PM2

Very rare variant in population databases, with high coverage;

PP5

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	Protein	UniProt
TMEM237	NM_001044385.3 linkuse as main transcript	c.52C>T	p.Arg18Ter	stop_gained	2/13	ENST00000409883.7	NP_001037850.1
TMEM237	NM_152388.4 linkuse as main transcript	c.28C>T	p.Arg10Ter	stop_gained	2/13		NP_689601.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TMEM237	ENST00000409883.7 linkuse as main transcript	c.52C>T	p.Arg18Ter	stop_gained	2/13	5	NM_001044385.3	ENSP00000386264	P4	Q96Q45-1

Frequencies

GnomAD3 genomes

AF:

0.0000592

AC:

AN:

152010

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000132

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.0000607

AC:

AN:

247028

Hom.:

AF XY:

0.0000448

AC XY:

AN XY:

133946

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0000332

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000125

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.0000731

AC:

106

AN:

1450636

Hom.:

Cov.:

AF XY:

0.0000763

AC XY:

AN XY:

720708

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0000118

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0000915

Gnomad4 OTH exome

AF:

0.0000668

GnomAD4 genome

AF:

0.0000592

AC:

AN:

152010

Hom.:

Cov.:

AF XY:

0.0000539

AC XY:

AN XY:

74232

show subpopulations

Gnomad4 AFR

AF:

0.00

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000132

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.0000926

Hom.:

Bravo

AF:

0.0000416

ESP6500AA

AF:

0.00

AC:

ESP6500EA

AF:

0.000368

AC:

ExAC

AF:

0.0000662

AC:

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:12

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Joubert syndrome 14

Pathogenic:6

Pathogenic, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	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	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, no assertion criteria provided	literature only	OMIM	Oct 05, 2012	- -
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. -
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	Revvity Omics, Revvity	Dec 29, 2021	- -

not provided

Pathogenic:3

Pathogenic, no assertion criteria provided	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	-	- -
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+	-	- -

TMEM237-related disorder

Pathogenic:1

Pathogenic, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Mar 19, 2024

The TMEM237 c.52C>T variant is predicted to result in premature protein termination (p.Arg18*). This variant is documented as causative for Joubert syndrome (Huang et al. 2011. PubMed ID: 22152675). Approximately 6% of Canadian Hutterites are carriers for this pathogenic variant (Huang et al. 2011. PubMed ID: 22152675). This variant is reported in 0.012% of alleles in individuals of European (Non-Finnish) descent in gnomAD. Nonsense variants in TMEM237 are expected to be pathogenic. This variant is interpreted as pathogenic. -

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: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Pathogenic

0.48

BayesDel_noAF

Pathogenic

0.60

CADD

Pathogenic

DANN

Uncertain

1.0

Eigen

Pathogenic

0.83

Eigen_PC

Pathogenic

0.69

FATHMM_MKL

Uncertain

0.96

MutationTaster

Benign

1.0

A;A

Vest4

0.25

GERP RS

3.9

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.060

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

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