NM_024514.5(CYP2R1):c.595C>T (p.Arg199Ter) AND Vitamin D hydroxylation-deficient rickets, type 1B

Germline classification:: Likely pathogenic (1 submission)
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV001806317.2

Allele description [Variation Report for NM_024514.5(CYP2R1):c.595C>T (p.Arg199Ter)]

NM_024514.5(CYP2R1):c.595C>T (p.Arg199Ter)

Genes:

CYP2R1:cytochrome P450 family 2 subfamily R member 1 [Gene - OMIM - HGNC]
PDE3B:phosphodiesterase 3B [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

11p15.2

Genomic location:

Preferred name:

NM_024514.5(CYP2R1):c.595C>T (p.Arg199Ter)

HGVS:

NC_000011.10:g.14880541G>A
NG_007936.1:g.16665C>T
NM_001377214.1:c.250C>T
NM_001377215.1:c.250C>T
NM_001377216.1:c.250C>T
NM_001377217.1:c.433C>T
NM_001377227.1:c.250C>T
NM_024514.5:c.595C>TMANE SELECT
NP_001364143.1:p.Arg84Ter
NP_001364144.1:p.Arg84Ter
NP_001364145.1:p.Arg84Ter
NP_001364146.1:p.Arg145Ter
NP_001364156.1:p.Arg84Ter
NP_078790.2:p.Arg199Ter
NC_000011.9:g.14902087G>A

Protein change:

R145*

Links:

dbSNP: rs782285382

NCBI 1000 Genomes Browser:

rs782285382

Molecular consequence:

NM_001377214.1:c.250C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001377215.1:c.250C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001377216.1:c.250C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001377217.1:c.433C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001377227.1:c.250C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_024514.5:c.595C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:: Vitamin D hydroxylation-deficient rickets, type 1B
Synonyms:: PSEUDOVITAMIN D3 DEFICIENCY RICKETS DUE TO 25-HYDROXYLASE DEFICIENCY; VITAMIN D-DEPENDENT RICKETS, TYPE 1B
Identifiers:: MONDO: MONDO:0010810; MedGen: C1838657; Orphanet: 289157; OMIM: 600081

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002053826	Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic	inherited	clinical testing	PubMed (2) [See all records that cite these PMIDs] 15128933, 25741868

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002053826

Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic

inherited

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	inherited	yes	not provided	not provided	not provided	3	not provided	clinical testing

Citations

PubMed

Genetic evidence that the human CYP2R1 enzyme is a key vitamin D 25-hydroxylase.

Cheng JB, Levine MA, Bell NH, Mangelsdorf DJ, Russell DW.

Proc Natl Acad Sci U S A. 2004 May 18;101(20):7711-5. Epub 2004 May 5.

PubMed [citation]

PMID:: 15128933
PMCID:: PMC419671

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee.

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India, SCV002053826.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	inherited	yes	3	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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