ClinVar Genomic variation as it relates to human health
NM_001258244.2(TMEM218):c.238C>T (p.Arg80Cys)
The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.
Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_001258244.2(TMEM218):c.238C>T (p.Arg80Cys)
Variation ID: 983527 Accession: VCV000983527.3
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 11q24.2 11: 125097716 (GRCh38) [ NCBI UCSC ] 11: 124967612 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
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First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.
Last submission Help The date of the most recent submission for each type of classification for this variant.
Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline Nov 6, 2020 Dec 31, 2022 Oct 5, 2021 - HGVS
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... more HGVS ... less HGVSNucleotide Protein Molecular
consequenceNM_001258244.2:c.238C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001245173.1:p.Arg80Cys missense NM_001080546.3:c.238C>T NP_001074015.1:p.Arg80Cys missense NM_001258238.2:c.238C>T NP_001245167.1:p.Arg80Cys missense NM_001258239.3:c.238C>T NP_001245168.2:p.Arg80Cys missense NM_001258240.2:c.238C>T NP_001245169.1:p.Arg80Cys missense NM_001258241.2:c.238C>T NP_001245170.1:p.Arg80Cys missense NM_001258242.3:c.238C>T NP_001245171.2:p.Arg80Cys missense NM_001258243.3:c.238C>T NP_001245172.2:p.Arg80Cys missense NM_001258245.2:c.238C>T NP_001245174.1:p.Arg80Cys missense NM_001258246.3:c.238C>T NP_001245175.2:p.Arg80Cys missense NM_001258247.2:c.238C>T NP_001245176.1:p.Arg80Cys missense NM_001387230.1:c.238C>T NP_001374159.1:p.Arg80Cys missense NM_001387231.1:c.238C>T NP_001374160.1:p.Arg80Cys missense NM_001387232.1:c.238C>T NP_001374161.1:p.Arg80Cys missense NM_001387233.1:c.238C>T NP_001374162.1:p.Arg80Cys missense NM_001387234.1:c.238C>T NP_001374163.1:p.Arg80Cys missense NM_001387235.1:c.238C>T NP_001374164.1:p.Arg80Cys missense NM_001387236.1:c.238C>T NP_001374165.1:p.Arg80Cys missense NM_001387237.1:c.238C>T NP_001374166.1:p.Arg80Cys missense NM_001387238.1:c.238C>T NP_001374167.1:p.Arg80Cys missense NM_001387239.1:c.238C>T NP_001374168.1:p.Arg80Cys missense NM_001387240.1:c.238C>T NP_001374169.1:p.Arg80Cys missense NM_001387241.1:c.238C>T NP_001374170.1:p.Arg80Cys missense NM_001387242.1:c.238C>T NP_001374171.1:p.Arg80Cys missense NM_001387244.1:c.238C>T NP_001374173.1:p.Arg80Cys missense NM_001387245.1:c.238C>T NP_001374174.1:p.Arg80Cys missense NM_001387246.1:c.238C>T NP_001374175.1:p.Arg80Cys missense NM_001387247.1:c.238C>T NP_001374176.1:p.Arg80Cys missense NM_001387248.1:c.238C>T NP_001374177.1:p.Arg80Cys missense NM_001387249.1:c.316C>T NP_001374178.1:p.Arg106Cys missense NM_001387250.1:c.157C>T NP_001374179.1:p.Arg53Cys missense NM_001387251.1:c.157C>T NP_001374180.1:p.Arg53Cys missense NM_001387252.1:c.157C>T NP_001374181.1:p.Arg53Cys missense NM_001387253.1:c.157C>T NP_001374182.1:p.Arg53Cys missense NM_001387254.1:c.157C>T NP_001374183.1:p.Arg53Cys missense NM_001387255.1:c.*53C>T 3 prime UTR NM_001387256.1:c.*53C>T 3 prime UTR NM_001387257.1:c.*53C>T 3 prime UTR NM_001387258.1:c.*53C>T 3 prime UTR NM_001387259.1:c.*53C>T 3 prime UTR NR_047586.2:n.385C>T non-coding transcript variant NR_047587.2:n.168C>T non-coding transcript variant NR_047588.2:n.528C>T non-coding transcript variant NR_047589.2:n.292C>T non-coding transcript variant NR_047590.2:n.465C>T non-coding transcript variant NR_047591.2:n.351C>T non-coding transcript variant NR_047592.2:n.431C>T non-coding transcript variant NR_170600.1:n.347C>T non-coding transcript variant NR_170601.1:n.246C>T non-coding transcript variant NR_170602.1:n.383C>T non-coding transcript variant NR_170603.1:n.199C>T non-coding transcript variant NR_170604.1:n.296C>T non-coding transcript variant NR_170605.1:n.216C>T non-coding transcript variant NR_170606.1:n.121C>T non-coding transcript variant NR_170607.1:n.170C>T non-coding transcript variant NR_170608.1:n.201C>T non-coding transcript variant NR_170609.1:n.327C>T non-coding transcript variant NR_170610.1:n.504C>T non-coding transcript variant NR_170611.1:n.534C>T non-coding transcript variant NR_170612.1:n.245C>T non-coding transcript variant NR_170613.1:n.342C>T non-coding transcript variant NC_000011.10:g.125097716G>A NC_000011.9:g.124967612G>A - Protein change
- R80C, R106C, R53C
- Other names
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R115C
- Canonical SPDI
- NC_000011.10:125097715:G:A
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Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
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Global minor allele
frequency (GMAF) HelpThe global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.
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Allele frequency
Help
The frequency of the allele represented by this VCV record.
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Exome Aggregation Consortium (ExAC) 0.00004
Trans-Omics for Precision Medicine (TOPMed) 0.00018
Trans-Omics for Precision Medicine (TOPMed) 0.00011
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00015
The Genome Aggregation Database (gnomAD), exomes 0.00004
The Genome Aggregation Database (gnomAD) 0.00009
- Links
Genes
| Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
Help
Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
|---|---|---|---|---|---|---|
| HI score
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The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
Help
The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
Help
The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
Help
The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene. |
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| TMEM218 | - | - |
GRCh38 GRCh37 |
16 | 78 | |
Conditions - Germline
| Condition
Help
The condition for this variant-condition (RCV) record in ClinVar. |
Classification
Help
The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions) |
Review status
Help
The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. |
Last evaluated
Help
The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
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The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
|---|---|---|---|---|
| Pathogenic (1) |
no assertion criteria provided
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Nov 5, 2020 | RCV001263490.1 | |
| Pathogenic (1) |
no assertion criteria provided
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Nov 5, 2020 | RCV001263493.1 | |
| Likely pathogenic (2) |
criteria provided, single submitter
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Oct 5, 2021 | RCV001729826.2 |
Submissions - Germline
| Classification
Help
The submitted germline classification for each SCV record. (Last evaluated) |
Review status
Help
Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria) |
Condition
Help
The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant. |
Submitter
Help
The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar. |
More information
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This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter. |
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Likely pathogenic
(Oct 05, 2021)
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criteria provided, single submitter
Method: clinical testing
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Joubert syndrome 39
Affected status: unknown
Allele origin:
unknown
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Fulgent Genetics, Fulgent Genetics
Accession: SCV002777978.1
First in ClinVar: Dec 31, 2022 Last updated: Dec 31, 2022 |
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Pathogenic
(Nov 05, 2020)
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no assertion criteria provided
Method: research
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Joubert syndrome
Affected status: yes
Allele origin:
paternal
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UW Hindbrain Malformation Research Program, University of Washington
Accession: SCV001441589.1
First in ClinVar: Nov 06, 2020 Last updated: Nov 06, 2020 |
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Pathogenic
(Nov 05, 2020)
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no assertion criteria provided
Method: research
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Meckel syndrome, type 4
Affected status: yes
Allele origin:
maternal
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UW Hindbrain Malformation Research Program, University of Washington
Accession: SCV001441592.1
First in ClinVar: Nov 06, 2020 Last updated: Nov 06, 2020 |
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Pathogenic
(Oct 12, 2021)
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no assertion criteria provided
Method: literature only
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JOUBERT SYNDROME 39
Affected status: not provided
Allele origin:
germline
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OMIM
Accession: SCV001977561.1
First in ClinVar: Oct 16, 2021 Last updated: Oct 16, 2021 |
Comment on evidence:
For discussion of the c.343C-T transition (c.343C-T, NM_001258243.1) in the TMEM218 gene, resulting in an arg115-to-cys substitution (R155C), that was found in compound heterozygous state … (more)
For discussion of the c.343C-T transition (c.343C-T, NM_001258243.1) in the TMEM218 gene, resulting in an arg115-to-cys substitution (R155C), that was found in compound heterozygous state in a patient with Joubert syndrome-39 (JBTS39; 619562) by Van De Weghe et al. (2021), see 619285.0001. Van De Weghe et al. (2021) also found homozygosity for the c.343C-T transition in 4 fetuses from 2 unrelated families (UW363 and CUMC) in which the pregnancies were terminated due to the finding of occipital encephalocele on prenatal imaging. Functional studies of this variant were not performed. (less)
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Germline Functional Evidence
| There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar. |
Citations for germline classification of this variant
Help| Title | Author | Journal | Year | Link |
|---|---|---|---|---|
| TMEM218 dysfunction causes ciliopathies, including Joubert and Meckel syndromes. | Van De Weghe JC | HGG advances | 2021 | PMID: 33791682 |
Text-mined citations for rs141744337 ...
HelpRecord last updated Jun 10, 2023
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.