NM_000376.3(VDR):c.1206C>A (p.Arg402=) AND Vitamin D-dependent rickets type II with alopecia

Germline classification:: Likely benign (2 submissions)
Last evaluated:: Sep 10, 2021
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV001111881.5

Allele description [Variation Report for NM_000376.3(VDR):c.1206C>A (p.Arg402=)]

NM_000376.3(VDR):c.1206C>A (p.Arg402=)

Gene:

VDR:vitamin D receptor [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

12q13.11

Genomic location:

Preferred name:

NM_000376.3(VDR):c.1206C>A (p.Arg402=)

HGVS:

NC_000012.12:g.47844824G>T
NG_008731.1:g.65208C>A
NM_000376.3:c.1206C>AMANE SELECT
NM_001017535.2:c.1206C>A
NM_001017536.2:c.1356C>A
NM_001364085.2:c.1206C>A
NM_001374661.1:c.1206C>A
NM_001374662.1:c.1206C>A
NP_000367.1:p.Arg402=
NP_001017535.1:p.Arg402=
NP_001017536.1:p.Arg452=
NP_001351014.1:p.Arg402=
NP_001361590.1:p.Arg402=
NP_001361591.1:p.Arg402=
NC_000012.11:g.48238607G>T
NC_000012.11:g.48238607G>T
NM_001017535.1:c.1206C>A

Links:

dbSNP: rs2229829

NCBI 1000 Genomes Browser:

rs2229829

Molecular consequence:

NM_000376.3:c.1206C>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001017535.2:c.1206C>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001017536.2:c.1356C>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001364085.2:c.1206C>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001374661.1:c.1206C>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001374662.1:c.1206C>A - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Name:: Vitamin D-dependent rickets type II with alopecia (VDDR2A)
Synonyms:: GENERALIZED RESISTANCE TO 1,25-DIHYDROXYVITAMIN D; HYPOCALCEMIC VITAMIN D-RESISTANT RICKETS; PDDR IIA; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0010186; MedGen: C0342646; Orphanet: 93160; OMIM: 277440

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001269488	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019)	Likely benign (Apr 27, 2017)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 21168462, 18159135 Citation Link,
SCV002796642	Fulgent Genetics, Fulgent Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely benign (Sep 10, 2021)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001269488

Illumina Laboratory Services, Illumina

criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)

Likely benign
(Apr 27, 2017)

germline

clinical testing

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

Citation Link,

SCV002796642

Fulgent Genetics, Fulgent Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely benign
(Sep 10, 2021)

unknown

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Vitamin D receptor gene methylation is associated with ethnicity, tuberculosis, and TaqI polymorphism.

Andraos C, Koorsen G, Knight JC, Bornman L.

Hum Immunol. 2011 Mar;72(3):262-8. doi: 10.1016/j.humimm.2010.12.010. Epub 2010 Dec 16.

PubMed [citation]

PMID:: 21168462
PMCID:: PMC3955023

Genetic variations of VDR/NR1I1 encoding vitamin D receptor in a Japanese population.

Ukaji M, Saito Y, Fukushima-Uesaka H, Maekawa K, Katori N, Kaniwa N, Yoshida T, Nokihara H, Sekine I, Kunitoh H, Ohe Y, Yamamoto N, Tamura T, Saijo N, Sawada J.

Drug Metab Pharmacokinet. 2007 Dec;22(6):462-7.

PubMed [citation]

PMID:: 18159135

See all PubMed Citations (3)

Details of each submission

From Illumina Laboratory Services, Illumina, SCV001269488.1

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

Description

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.

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

From Fulgent Genetics, Fulgent Genetics, SCV002796642.1

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

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

Last Updated: Sep 29, 2024

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