ClinVar Genomic variation as it relates to human health
NM_024753.5(TTC21B):c.626C>T (p.Pro209Leu)
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_024753.5(TTC21B):c.626C>T (p.Pro209Leu)
Variation ID: 30935 Accession: VCV000030935.34
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 2q24.3 2: 165941111 (GRCh38) [ NCBI UCSC ] 2: 166797621 (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 Oct 11, 2015 Oct 8, 2024 Jan 14, 2024 - HGVS
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Nucleotide Protein Molecular
consequenceNM_024753.5:c.626C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_079029.3:p.Pro209Leu missense NC_000002.12:g.165941111G>A NC_000002.11:g.166797621G>A NG_030345.1:g.17728C>T Q7Z4L5:p.Pro209Leu - Protein change
- P209L
- Other names
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- Canonical SPDI
- NC_000002.12:165941110: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) 0.00007
The Genome Aggregation Database (gnomAD) 0.00011
The Genome Aggregation Database (gnomAD), exomes 0.00013
Trans-Omics for Precision Medicine (TOPMed) 0.00014
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00015
- 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 | ||
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HI score
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The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
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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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TTC21B | - | - |
GRCh38 GRCh37 |
1123 | 1326 | |
TTC21B-AS1 | - | - | - | GRCh38 | - | 152 |
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
Help
The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
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Pathogenic/Likely pathogenic (6) |
criteria provided, multiple submitters, no conflicts
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Dec 1, 2022 | RCV000023924.13 | |
Pathogenic (6) |
criteria provided, multiple submitters, no conflicts
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Apr 25, 2022 | RCV000681870.12 | |
Pathogenic (1) |
criteria provided, single submitter
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Jan 14, 2024 | RCV000685092.5 | |
Pathogenic (1) |
criteria provided, single submitter
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May 19, 2022 | RCV000763456.3 | |
Pathogenic (1) |
no assertion criteria provided
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Nov 21, 2018 | RCV000786982.2 | |
Pathogenic (1) |
criteria provided, single submitter
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Jan 28, 2019 | RCV000857219.1 | |
Likely pathogenic (1) |
no assertion criteria provided
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Jun 23, 2019 | RCV001003236.1 | |
Pathogenic (1) |
criteria provided, single submitter
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Sep 22, 2017 | RCV001074967.2 | |
Pathogenic/Likely pathogenic (2) |
no assertion criteria provided
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May 3, 2018 | RCV001328175.2 | |
See cases
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Pathogenic (1) |
criteria provided, single submitter
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May 10, 2021 | RCV002251925.2 |
TTC21B-related disorder
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Pathogenic (1) |
no assertion criteria provided
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Aug 30, 2024 | RCV004528134.2 |
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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
Help
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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Pathogenic
(Jun 26, 2017)
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criteria provided, single submitter
Method: research
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Nephronophthisis 12
(Autosomal recessive inheritance)
Affected status: yes
Allele origin:
germline
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Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard
Study: Broad Institute Center for Mendelian Genomics (CMG)
Accession: SCV000693904.1 First in ClinVar: Oct 11, 2015 Last updated: Oct 11, 2015 |
Comment:
Previously reported homozygous missense mutation (p.P209L) in the TTC21B gene in seven families with FSGS (PMID: 26940125).
Number of individuals with the variant: 1
Clinical Features:
Cystic kidney disease (present) , Enlarged-cystic kidneys (present) , Congenital liver fibrosis (present)
Ethnicity/Population group: Caucasian
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Pathogenic
(Sep 16, 2018)
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criteria provided, single submitter
Method: research
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not provided
Affected status: yes
Allele origin:
germline
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Gharavi Laboratory, Columbia University
Accession: SCV000809349.1
First in ClinVar: Oct 01, 2018 Last updated: Oct 01, 2018 |
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Pathogenic
(Jan 01, 2015)
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criteria provided, single submitter
Method: clinical testing
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Nephronophthisis 12
Affected status: yes
Allele origin:
inherited
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Equipe Genetique des Anomalies du Developpement, Université de Bourgogne
Accession: SCV000965772.1
First in ClinVar: Aug 26, 2019 Last updated: Aug 26, 2019 |
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Pathogenic
(May 10, 2021)
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criteria provided, single submitter
Method: clinical testing
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See cases
Affected status: yes
Allele origin:
germline
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Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein
Accession: SCV002523162.1
First in ClinVar: Jun 09, 2022 Last updated: Jun 09, 2022 |
Comment:
ACMG classification criteria: PS3, PM3, PP1, PP3
Clinical Features:
Interstitial nephritis (present) , Renal insufficiency (present) , Hyperuricosuria (present) , Hyperuricemia (present) , Abnormal renal tubule morphology (present) , Abnormal renal insterstitial morphology (present)
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Pathogenic
(May 19, 2022)
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criteria provided, single submitter
Method: clinical testing
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Asphyxiating thoracic dystrophy 4
Nephronophthisis 12
Affected status: unknown
Allele origin:
unknown
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Fulgent Genetics, Fulgent Genetics
Accession: SCV000894233.2
First in ClinVar: Mar 31, 2019 Last updated: Dec 31, 2022 |
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Pathogenic
(Dec 01, 2022)
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criteria provided, single submitter
Method: clinical testing
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Nephronophthisis 12
Affected status: yes
Allele origin:
biparental
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Eurofins-Biomnis
Accession: SCV003935133.1
First in ClinVar: Jun 24, 2023 Last updated: Jun 24, 2023 |
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Pathogenic
(Nov 24, 2019)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
germline
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Revvity Omics, Revvity
Accession: SCV002022453.3
First in ClinVar: Nov 29, 2021 Last updated: Feb 04, 2024 |
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Pathogenic
(Jan 14, 2024)
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criteria provided, single submitter
Method: clinical testing
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Jeune thoracic dystrophy
Nephronophthisis
Explanation for multiple conditions: Uncertain.
The variant was classified for several related diseases, possibly a spectrum of disease; the variant may be associated with one or more the diseases.
Affected status: unknown
Allele origin:
germline
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Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV000812564.4
First in ClinVar: Oct 10, 2018 Last updated: Feb 28, 2024 |
Comment:
This sequence change replaces proline, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 209 of the TTC21B protein (p.Pro209Leu). … (more)
This sequence change replaces proline, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 209 of the TTC21B protein (p.Pro209Leu). This variant is present in population databases (rs140511594, gnomAD 0.08%). This missense change has been observed in individual(s) with focal segmental glomerulosclerosis and nephronophthisis (PMID: 21258341, 24876116). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 30935). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on TTC21B protein function. Experimental studies have shown that this missense change affects TTC21B function (PMID: 21258341, 24876116). For these reasons, this variant has been classified as Pathogenic. (less)
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Pathogenic
(Jan 28, 2019)
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criteria provided, single submitter
Method: clinical testing
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Infantile nephronophthisis
Affected status: yes
Allele origin:
maternal
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Center of Genomic medicine, Geneva, University Hospital of Geneva
Accession: SCV000999803.1
First in ClinVar: Dec 17, 2019 Last updated: Dec 17, 2019 |
Comment:
This variant was identified in composite heterozygosity with another variant in the same gene in a female patient with nephronophtisis, retinopathy and suspected ciliopathy
Number of individuals with the variant: 2
Age: 30-39 years
Sex: female
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Pathogenic
(Sep 22, 2017)
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criteria provided, single submitter
Method: clinical testing
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Retinal dystrophy
Affected status: yes
Allele origin:
germline
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Blueprint Genetics
Accession: SCV001240574.1
First in ClinVar: Apr 18, 2020 Last updated: Apr 18, 2020
Comment:
My Retina Tracker patient
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Likely pathogenic
(Feb 01, 2020)
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criteria provided, single submitter
Method: research
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Nephronophthisis 12
Affected status: yes
Allele origin:
inherited
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Molecular Biology Laboratory, Fundació Puigvert
Study: KidneyPanel_2020
Accession: SCV001425282.1 First in ClinVar: Jan 17, 2021 Last updated: Jan 17, 2021 |
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Pathogenic
(Apr 25, 2022)
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criteria provided, single submitter
Method: clinical testing
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Not Provided
Affected status: yes
Allele origin:
germline
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GeneDx
Accession: SCV001805755.3
First in ClinVar: Aug 21, 2021 Last updated: Mar 04, 2023 |
Comment:
Published functional studies demonstrate a damaging effect (Huynh Cong et al., 2014); In silico analysis supports that this missense variant has a deleterious effect on … (more)
Published functional studies demonstrate a damaging effect (Huynh Cong et al., 2014); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 24876116, 21258341, 29127259, 31456290, 32714622, 33599192, 34426522, 33712733, 31589614, 33226606, 33547761, 33532864, 26940125) (less)
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Pathogenic
(Mar 01, 2011)
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no assertion criteria provided
Method: literature only
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NEPHRONOPHTHISIS 12
Affected status: not provided
Allele origin:
germline
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OMIM
Accession: SCV000045215.2
First in ClinVar: Apr 04, 2013 Last updated: Jun 21, 2018 |
Comment on evidence:
In affected members of 2 unrelated consanguineous families with nephronophthisis-12 (NPHP12; 613820), Davis et al. (2011) identified a homozygous mutation in exon 6 of the … (more)
In affected members of 2 unrelated consanguineous families with nephronophthisis-12 (NPHP12; 613820), Davis et al. (2011) identified a homozygous mutation in exon 6 of the TTC21B gene, resulting in a pro209-to-leu (P209L) substitution in a TPR domain. One family was of Portuguese and the other of Egyptian descent. The mutation was not found in 796 controls. In vitro and in vivo functional expression studies in mammalian cells and zebrafish indicated that the mutant protein was a hypomorphic allele. In 2 additional families with early-onset NPHP with extrarenal manifestations, the P209L allele was found in compound heterozygosity with another pathogenic TTC21B allele: a cys552-to-ter (C552X; 612014.0002) substitution in exon 13 and an A-to-G transition in intron 20 (612014.0003), respectively. Both of the latter mutations were shown by expression studies to be functionally null alleles. Haplotype analysis indicated a founder effect for the P209L allele. (less)
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Pathogenic
(-)
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no assertion criteria provided
Method: clinical testing
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not provided
Affected status: yes
Allele origin:
germline
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Genome Diagnostics Laboratory, Amsterdam University Medical Center
Study: VKGL Data-share Consensus
Accession: SCV001807047.1 First in ClinVar: Aug 27, 2021 Last updated: Aug 27, 2021 |
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Pathogenic
(-)
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no assertion criteria provided
Method: clinical testing
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not provided
Affected status: yes
Allele origin:
germline
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Genome Diagnostics Laboratory, University Medical Center Utrecht
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001929844.1 First in ClinVar: Sep 24, 2021 Last updated: Sep 24, 2021 |
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Likely pathogenic
(-)
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no assertion criteria provided
Method: clinical testing
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not provided
Affected status: yes
Allele origin:
germline
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Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001952961.1 First in ClinVar: Oct 02, 2021 Last updated: Oct 02, 2021 |
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Pathogenic
(-)
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no assertion criteria provided
Method: research
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Nephronophthisis 12
Affected status: yes
Allele origin:
unknown
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Genomics And Bioinformatics Analysis Resource, Columbia University
Accession: SCV004024139.1
First in ClinVar: Aug 13, 2023 Last updated: Aug 13, 2023
Comment:
Compound Heterozygous
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Pathogenic
(Aug 30, 2024)
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no assertion criteria provided
Method: clinical testing
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TTC21B-related condition
Affected status: unknown
Allele origin:
germline
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PreventionGenetics, part of Exact Sciences
Accession: SCV004107728.2
First in ClinVar: Nov 20, 2023 Last updated: Oct 08, 2024 |
Comment:
The TTC21B c.626C>T variant is predicted to result in the amino acid substitution p.Pro209Leu. This variant was reported in the homozygous or compound heterozygous state … (more)
The TTC21B c.626C>T variant is predicted to result in the amino acid substitution p.Pro209Leu. This variant was reported in the homozygous or compound heterozygous state in multiple individuals with nephronophthisis or focal segmental glomerulosclerosis (FSGS) (Davis et al. 2011. PubMed ID: 21258341; Bullich et al. 2017. PubMed ID: 26940125; Cong et al. 2014. PubMed ID: 24876116). This variant is reported in 0.077% of alleles in individuals of Ashkenazi Jewish descent in gnomAD and has been interpreted in ClinVar as pathogenic/likely pathogenic by multiple submitters (https://preview.ncbi.nlm.nih.gov/clinvar/variation/30935/). This variant is interpreted as pathogenic. (less)
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Pathogenic
(Nov 21, 2018)
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no assertion criteria provided
Method: clinical testing
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Finnish congenital nephrotic syndrome
Affected status: yes
Allele origin:
germline
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Bioscientia Institut fuer Medizinische Diagnostik GmbH, Sonic Healthcare
Accession: SCV000925888.1
First in ClinVar: Jul 14, 2019 Last updated: Jul 14, 2019 |
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Likely pathogenic
(Jun 23, 2019)
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no assertion criteria provided
Method: research
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Senior Loken syndrome
Affected status: yes
Allele origin:
inherited
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Sharon lab, Hadassah-Hebrew University Medical Center
Accession: SCV001161315.1
First in ClinVar: Feb 16, 2020 Last updated: Feb 16, 2020 |
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Pathogenic
(May 03, 2018)
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no assertion criteria provided
Method: clinical testing
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Nephrotic syndrome
Affected status: yes
Allele origin:
unknown
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Sydney Genome Diagnostics, Children's Hospital Westmead
Accession: SCV001449463.1
First in ClinVar: Mar 22, 2021 Last updated: Mar 22, 2021 |
Comment:
This patient is homozygous for a known pathogenic variant, c.626C>T p.(Pro209Leu), in the TTC21B gene. This variant (dbSNP: rs140511594), in the homozygous state, has been … (more)
This patient is homozygous for a known pathogenic variant, c.626C>T p.(Pro209Leu), in the TTC21B gene. This variant (dbSNP: rs140511594), in the homozygous state, has been previously reported in patients with nephronophthisis and focal segmental glomerulosclerosis (FSGS) (Davis et al 2011 Nat Genet 43:189-196; Cong et al 2014 J Am Soc Nephrol 25:2435-2443; Bullich et al 2017 Nephrol Dial Transplant 32:151-156). Bullich et al 2017 also reported hypertension in some patients homozygous for p.(Pro209Leu). This variant was found in patients of North Africian or Portuguese descent. Functional studies showed the p.Pro209Leu variant partially altered cilia structure, cell migration and cytoskeleton suggesting a hypomorphic allele (Davis et al 2011; Cong et al 2014; Bullich et al 2017). This variant is considered to be pathogenic according to the ACMG guidelines. (less)
Number of individuals with the variant: 1
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Likely pathogenic
(Nov 10, 2017)
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no assertion criteria provided
Method: literature only
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Nephrotic syndrome
Affected status: yes
Allele origin:
germline
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Yale Center for Mendelian Genomics, Yale University
Study: Yale Center for Mendelian Genomics
Accession: SCV002107060.1 First in ClinVar: Mar 28, 2022 Last updated: Mar 28, 2022 |
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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
HelpTitle | Author | Journal | Year | Link |
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Clinical utility of genetic testing in early-onset kidney disease: seven genes are the main players. | Domingo-Gallego A | Nephrology, dialysis, transplantation : official publication of the European Dialysis and Transplant Association - European Renal Association | 2022 | PMID: 33532864 |
Whole Exome Sequencing of Patients with Steroid-Resistant Nephrotic Syndrome. | Warejko JK | Clinical journal of the American Society of Nephrology : CJASN | 2018 | PMID: 29127259 |
Contribution of the TTC21B gene to glomerular and cystic kidney diseases. | Bullich G | Nephrology, dialysis, transplantation : official publication of the European Dialysis and Transplant Association - European Renal Association | 2017 | PMID: 26940125 |
A homozygous missense mutation in the ciliary gene TTC21B causes familial FSGS. | Huynh Cong E | Journal of the American Society of Nephrology : JASN | 2014 | PMID: 24876116 |
TTC21B contributes both causal and modifying alleles across the ciliopathy spectrum. | Davis EE | Nature genetics | 2011 | PMID: 21258341 |
Text-mined citations for rs140511594 ...
HelpRecord last updated Nov 03, 2024
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.