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NM_152443.3(RDH12):c.164C>T (p.Thr55Met)

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Interpretation:
Pathogenic/Likely pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
5 (Most recent: Jul 4, 2021)
Last evaluated:
Aug 27, 2020
Accession:
VCV000805928.10
Variation ID:
805928
Description:
single nucleotide variant
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NM_152443.3(RDH12):c.164C>T (p.Thr55Met)

Allele ID
794252
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
14q24.1
Genomic location
14: 67724568 (GRCh38) GRCh38 UCSC
14: 68191285 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000014.8:g.68191285C>T
NC_000014.9:g.67724568C>T
NG_008321.1:g.27683C>T
... more HGVS
Protein change
T55M
Other names
-
Canonical SPDI
NC_000014.9:67724567:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00002
Exome Aggregation Consortium (ExAC) 0.00003
Links
dbSNP: rs766631462
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic/Likely pathogenic 3 criteria provided, multiple submitters, no conflicts Aug 27, 2020 RCV000993753.3
Pathogenic 1 criteria provided, single submitter Oct 1, 2016 RCV001091052.2
Pathogenic 1 no assertion criteria provided Jun 23, 2019 RCV001003153.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
RDH12 - - GRCh38
GRCh37
188 298

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely pathogenic
(May 29, 2020)
criteria provided, single submitter
Method: research
Leber congenital amaurosis 13
(Autosomal recessive inheritance)
Allele origin: germline
Broad Institute Rare Disease Group, Broad Institute
Accession: SCV001430808.1
Submitted: (May 29, 2020)
Evidence details
Publications
PubMed (2)
Other databases
https://erepo.clinicalgenome.org…
Comment:
The heterozygous p.Thr55Met variant in RDH12 was identified by our study in 1 individual with leber congenital amaurosis, in a compound heterozygous state with a … (more)
Pathogenic
(Aug 27, 2020)
criteria provided, single submitter
Method: clinical testing
Leber congenital amaurosis 13
Allele origin: germline
Invitae
Accession: SCV001586236.1
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (4)
Comment:
This sequence change replaces threonine with methionine at codon 55 of the RDH12 protein (p.Thr55Met). The threonine residue is highly conserved and there is a … (more)
Pathogenic
(Oct 01, 2016)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
CeGaT Praxis fuer Humangenetik Tuebingen
Accession: SCV001246889.6
Submitted: (Jul 04, 2021)
Evidence details
Likely pathogenic
(Aug 01, 2019)
no assertion criteria provided
Method: clinical testing
Leber congenital amaurosis 13
Allele origin: germline
Ocular Genomics Institute, Massachusetts Eye and Ear
Accession: SCV001146946.1
Submitted: (Aug 30, 2019)
Evidence details
Pathogenic
(Jun 23, 2019)
no assertion criteria provided
Method: research
Leber congenital amaurosis
Allele origin: inherited
Sharon lab,Hadassah-Hebrew University Medical Center
Accession: SCV001161222.1
Submitted: (Jun 25, 2019)
Evidence details

Functional evidence

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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 this variant

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Title Author Journal Year Link
Expanding the phenotypic spectrum in RDH12-associated retinal disease. Scott HA Cold Spring Harbor molecular case studies 2020 PMID: 32014858
The co-occurrence of rare non-ocular phenotypes in patients with inherited retinal degenerations. Ehrenberg M Molecular vision 2019 PMID: 31814694
Phenotype-genotype correlation with Sanger sequencing identified retinol dehydrogenase 12 (RDH12) compound heterozygous variants in a Chinese family with Leber congenital amaurosis. Li Y Journal of Zhejiang University. Science. B 2017 PMID: 28471114
Comprehensive molecular diagnosis of 179 Leber congenital amaurosis and juvenile retinitis pigmentosa patients by targeted next generation sequencing. Wang X Journal of medical genetics 2013 PMID: 23847139
Retinal degeneration associated with RDH12 mutations results from decreased 11-cis retinal synthesis due to disruption of the visual cycle. Thompson DA Human molecular genetics 2005 PMID: 16269441
https://erepo.clinicalgenome.org/evrepo/ui/interpretation/ebf7ef2b-52d1-4b9a-9f0a-efcc14117211 - - - -

Text-mined citations for rs766631462...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Nov 27, 2021