rs137853108

Variant summary

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

The NM_153704.6(TMEM67):c.622A>T(p.Arg208Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000298 in 1,613,342 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 0.00024 ( 0 hom., cov: 32)

Exomes 𝑓: 0.00030 ( 0 hom. )

Consequence

TMEM67
NM_153704.6 stop_gained

Scores

Clinical Significance

Pathogenic criteria provided, multiple submitters, no conflicts P:20

Conservation

PhyloP100: 0.428

Variant links:

Genes affected

TMEM67 (HGNC:28396): (transmembrane protein 67) The protein encoded by this gene localizes to the primary cilium and to the plasma membrane. The gene functions in centriole migration to the apical membrane and formation of the primary cilium. Multiple transcript variants encoding different isoforms have been found for this gene. Defects in this gene are a cause of Meckel syndrome type 3 (MKS3) and Joubert syndrome type 6 (JBTS6). [provided by RefSeq, Nov 2008]

TMEM67 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 8-93765617-A-T is Pathogenic according to our data. Variant chr8-93765617-A-T is described in ClinVar as [Pathogenic]. Clinvar id is 1376.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-93765617-A-T is described in Lovd as [Pathogenic]. Variant chr8-93765617-A-T is described in Lovd as [Pathogenic]. Variant chr8-93765617-A-T is described in Lovd as [Likely_pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TMEM67	NM_153704.6 linkuse as main transcript	c.622A>T	p.Arg208Ter	stop_gained	6/28	ENST00000453321.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TMEM67	ENST00000453321.8 linkuse as main transcript	c.622A>T	p.Arg208Ter	stop_gained	6/28	1	NM_153704.6	P1

Frequencies

GnomAD3 genomes

AF:

0.000236

AC:

AN:

152238

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000482

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:

0.000485

Gnomad OTH

AF:

0.000478

GnomAD3 exomes

AF:

0.000175

AC:

AN:

251386

Hom.:

AF XY:

0.000191

AC XY:

AN XY:

135876

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.0000289

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000378

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.000304

AC:

444

AN:

1461104

Hom.:

Cov.:

AF XY:

0.000300

AC XY:

218

AN XY:

726958

show subpopulations

Gnomad4 AFR exome

AF:

0.0000897

Gnomad4 AMR exome

AF:

0.0000224

Gnomad4 ASJ exome

AF:

0.0000383

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.0000187

Gnomad4 NFE exome

AF:

0.000390

Gnomad4 OTH exome

AF:

0.0000828

GnomAD4 genome

AF:

0.000236

AC:

AN:

152238

Hom.:

Cov.:

AF XY:

0.000134

AC XY:

AN XY:

74380

show subpopulations

Gnomad4 AFR

AF:

0.0000482

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:

0.000485

Gnomad4 OTH

AF:

0.000478

Alfa

AF:

0.000244

Hom.:

Bravo

AF:

0.000219

TwinsUK

AF:

0.000809

AC:

ALSPAC

AF:

0.000519

AC:

ESP6500AA

AF:

0.00

AC:

ESP6500EA

AF:

0.000116

AC:

ExAC

AF:

0.000140

AC:

EpiCase

AF:

0.000218

EpiControl

AF:

0.000237

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:20

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Pathogenic:7

Pathogenic, no assertion criteria provided	clinical testing	Genome Diagnostics Laboratory, University Medical Center Utrecht	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	May 13, 2022	Nonsense 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: 19508969, 17397051, 31974414, 23352055, 26092869, 23559409, 26729329, 25525159, 17377820, 21866095, 25920555, 28973083, 29891882, 28680603, 28497568, 29146704, 34426522, 31589614) -
Pathogenic, no assertion criteria provided	clinical testing	Clinical Genetics, Academic Medical Center	-	- -
Pathogenic, no assertion criteria provided	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	May 04, 2021	- -
Pathogenic, no assertion criteria provided	clinical testing	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Jul 25, 2016	- -

Joubert syndrome 6

Pathogenic:4

Pathogenic, criteria provided, single submitter	clinical testing	Genetic Services Laboratory, University of Chicago	Oct 16, 2014	- -
Pathogenic, criteria provided, single submitter	research	UW Hindbrain Malformation Research Program, University of Washington	Feb 23, 2015	- -
Pathogenic, no assertion criteria provided	literature only	OMIM	Oct 01, 2009	- -
Pathogenic, criteria provided, single submitter	clinical testing	Institute of Human Genetics, University of Leipzig Medical Center	Nov 10, 2021	This variant was identified as compound heterozygous with NM_153704.6:c.2374A>G._x000D_ Criteria applied: PVS1, PS4 -

RHYNS syndrome

Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Centre for Mendelian Genomics, University Medical Centre Ljubljana	Sep 11, 2019	This variant was classified as: Pathogenic. The following ACMG criteria were applied in classifying this variant: PVS1,PP5. -
Pathogenic, no assertion criteria provided	literature only	OMIM	Oct 01, 2009	- -

TMEM67-related disorder

Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego	-	This variant results in a c.379A>T (p.Arg127Ter) change in an alternate TMEM67 transcript NM_001142301. This gene is also known as MKS3 in the literature (PMID: 17397051). This nonsense variant found in exon 7 of 28 is predicted to result in loss of normal protein function through either protein truncation or nonsense-mediated mRNA decay (NMD). This variant has been previously reported in the compound heterozygous state in individuals with Joubert Syndrome, Meckel-Gruber syndrome, and nephronophthisis (PMID: 17397051, 21866095, 26092869, 17377820, 23559409). Loss-of-function variation in TMEM67 has been reported in affected individuals in the literature (PMID: 17397051, 21866095, 26092869, 17377820, 23559409). The c.622A>T (p.Arg208Ter) variant is present in the heterozygous state in the gnomAD population database at a frequency of 0.017% (49/282,794). Based on the available evidence, the c.622A>T (p.Arg208Ter) variant is classified as Pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Apr 27, 2017	The TMEM67 c.622A>T (p.Arg208Ter) variant is a stop-gained variant and is predicted result in premature termination of the TMEM67 protein. Across a selection of available literature, the p.Arg208Ter variant has been identified in 12 patients with a phenotype of nephronophthisis, Joubert syndrome, or Meckel syndrome, including in a compound heterozygous state in nine patients and in a heterozygous state in three affected patients in whom a second variant was not identified, and in a heterozygous state in seven unaffected family members (Consugar et al. 2007; Khaddour et al. 2007; Otto et al. 2009; Halbritter et al. 2013). The p.Arg208Ter variant was absent from 388 controls and is reported at a frequency of 0.00024 in the European (non-Finnish) population of the Exome Aggregation Consortium. Based on the evidence and the potential impact of stop-gained variants, the p.Arg208Ter variant is classified as pathogenic for TMEM67-related disorders. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population. -

Meckel-Gruber syndrome;C0431399:Familial aplasia of the vermis

Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Invitae

Jan 19, 2024

This sequence change creates a premature translational stop signal (p.Arg208*) in the TMEM67 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in TMEM67 are known to be pathogenic (PMID: 20232449, 23559409). This variant is present in population databases (rs137853108, gnomAD 0.04%). This premature translational stop signal has been observed in individuals with Joubert syndrome, Meckel-Gruber syndrome, and/or nephronophthisis-related ciliopathies (PMID: 17377820, 17397051, 21866095, 23559409, 26092869). ClinVar contains an entry for this variant (Variation ID: 1376). For these reasons, this variant has been classified as Pathogenic. -

Meckel syndrome, type 3

Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

Oct 01, 2009

- -

Inborn genetic diseases

Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Jun 09, 2023

The c.622A>T (p.R208*) alteration, located in exon 6 (coding exon 6) of the TMEM67 gene, consists of an A to T substitution at nucleotide position 622. This changes the amino acid from an arginine (R) to a stop codon at amino acid position 208. This alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. Based on data from gnomAD, the T allele has an overall frequency of 0.017% (49/282794) total alleles studied. The highest observed frequency was 0.037% (48/129126) of European (non-Finnish) alleles. This variant has been detected in conjunction with other variants in the TMEM67 gene in multiple individuals diagnosed with clinical features associated with TMEM67-related ciliopathies; however, the phase of the two variants is either unspecified or confirmed in trans (opposite chromosome) (Otto, 2009; Khaddour, 2007; Chaki, 2011; Szymanska, 2012; Bachmann-Gagescu, 2015; Summers, 2017; Vogel, 2017; Meng, 2017). Based on the available evidence, this alteration is classified as pathogenic. -

Meckel syndrome, type 3;C1853153:Joubert syndrome 6;C1865794:RHYNS syndrome;C2673874:Bardet-Biedl syndrome 14;C3150796:Nephronophthisis 11;C5435651:COACH syndrome 1

Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Fulgent Genetics, Fulgent Genetics

May 26, 2022

- -

Joubert syndrome and related disorders

Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Sep 09, 2022

Variant summary: TMEM67 c.622A>T (p.Arg208X) 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 by our laboratory. The variant allele was found at a frequency of 0.00018 in 251386 control chromosomes (gnomAD). This frequency is not higher than expected for a pathogenic variant in TMEM67 causing Joubert Syndrome And Related Disorders (0.00018 vs 0.0018), allowing no conclusion about variant significance. c.622A>T has been reported in the literature in multiple individuals affected with Joubert Syndrome, Meckel-Gruber syndrome and nephronophthisis-related ciliopathies (e.g. Consugar_2007, Halbritter_2013, Fleming_2017). These data indicate that the variant is very likely to be associated with disease. Eight ClinVar submitters (evaluation after 2014) cite the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Pathogenic

0.40

BayesDel_noAF

Pathogenic

0.15

Cadd

Pathogenic

Dann

Benign

0.97

Eigen

Benign

-0.0083

Eigen_PC

Benign

-0.36

FATHMM_MKL

Benign

0.037

MutationTaster

Benign

1.0

A;A

Vest4

0.76, 0.63

GERP RS

-4.0

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.080

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

Other links and lift over