NM_024514.5:c.296T>C

Variant names:

• chr11-14885847-A-G
• rs61495246
• NM_024514.5:c.296T>C

Variant summary

Our verdict is Likely pathogenic. The variant received 8 ACMG points: 9P and 1B. PP3 PP5_Very_Strong BP4

The NM_024514.5(CYP2R1):​c.296T>C​(p.Leu99Pro) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000193 in 1,613,700 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★).

• Frequency:
  • Genomes: 𝑓 0.0010 (0 hom., cov: 32)
  • Exomes 𝑓: 0.00011 (0 hom.)
• Consequence: CYP2R1 NM_024514.5 missense
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:10
• Conservation: PhyloP100: 9.32
• Publications: 30 publications found

Genes affected

CYP2R1 (HGNC:20580): (cytochrome P450 family 2 subfamily R member 1) This gene encodes a member of the cytochrome P450 superfamily of enzymes. The cytochrome P450 proteins are monooxygenases which catalyze many reactions involved in drug metabolism and synthesis of cholesterol, steroids and other lipids. This enzyme is a microsomal vitamin D hydroxylase that converts vitamin D into the active ligand for the vitamin D receptor. A mutation in this gene has been associated with selective 25-hydroxyvitamin D deficiency. [provided by RefSeq, Jul 2008]

PDE3B (HGNC:8779): (phosphodiesterase 3B) Enables 3',5'-cyclic-nucleotide phosphodiesterase activity. Involved in negative regulation of angiogenesis; negative regulation of cell adhesion; and negative regulation of lipid catabolic process. Located in membrane. Part of guanyl-nucleotide exchange factor complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_pathogenic. The variant received 8 ACMG points.

• PP3: Multiple lines of computational evidence support a deleterious effect 10: AlphaMissense, BayesDel_noAF, Cadd, Dann, Eigen, MutationAssessor, phyloP100way_vertebrate, PROVEAN, REVEL, REVEL [when max_spliceai, FATHMM_MKL, MetaRNN, MutationTaster was below the threshold]
• PP5: Variant 11-14885847-A-G is Pathogenic according to our data. Variant chr11-14885847-A-G is described in ClinVar as Pathogenic/Likely_pathogenic. ClinVar VariationId is 2134.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BP4: Computational evidence support a benign effect (MetaRNN=0.09614125). . Strength limited to SUPPORTING due to the PP5.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CYP2R1	NM_024514.5	c.296T>C	p.Leu99Pro	missense_variant	Exon 2 of 5	ENST00000334636.10	NP_078790.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CYP2R1	ENST00000334636.10	c.296T>C	p.Leu99Pro	missense_variant	Exon 2 of 5	1	NM_024514.5	ENSP00000334592.5
CYP2R1	ENST00000532805.1	n.6T>C		non_coding_transcript_exon_variant	Exon 1 of 4	5		ENSP00000465097.1

Frequencies

GnomAD3 genomes AF: 0.00103 AC: 157 AN: 152210 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.00371

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000655

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.000478

GnomAD2 exomes AF: 0.000243 AC: 61 AN: 251224 AF XY: 0.000133

Gnomad AFR exome AF: 0.00345

Gnomad AMR exome AF: 0.000145

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.000105 AC: 154 AN: 1461372 Hom.: 0 Cov.: 31 AF XY: 0.0000935 AC XY: 68 AN XY: 726972

African (AFR) AF: 0.00394 AC: 132 AN: 33468

American (AMR) AF: 0.000157 AC: 7 AN: 44696

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26116

East Asian (EAS) AF: 0.00 AC: 0 AN: 39674

South Asian (SAS) AF: 0.00 AC: 0 AN: 86238

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53402

Middle Eastern (MID) AF: 0.000177 AC: 1 AN: 5646

European-Non Finnish (NFE) AF: 0.00000540 AC: 6 AN: 1111758

Other (OTH) AF: 0.000133 AC: 8 AN: 60374

GnomAD4 genome AF: 0.00103 AC: 157 AN: 152328 Hom.: 0 Cov.: 32 AF XY: 0.000980 AC XY: 73 AN XY: 74488

African (AFR) AF: 0.00370 AC: 154 AN: 41576

American (AMR) AF: 0.0000654 AC: 1 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5190

South Asian (SAS) AF: 0.000207 AC: 1 AN: 4828

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10630

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 68018

Other (OTH) AF: 0.000473 AC: 1 AN: 2116

Alfa AF: 0.000306 Hom.: 0

Bravo AF: 0.00119

ESP6500AA AF: 0.00455 AC: 20

ESP6500EA AF: 0.00 AC: 0

ExAC AF: 0.000346 AC: 42

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:10

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Vitamin D hydroxylation-deficient rickets, type 1B Pathogenic:6

May 18, 2004

OMIM

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

- -

Apr 24, 2024

Fulgent Genetics, Fulgent Genetics

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Feb 27, 2023

Department of Pathology and Laboratory Medicine, Sinai Health System

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: research

- -

Apr 09, 2021

Baylor Genetics

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jan 13, 2023

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant summary: CYP2R1 c.296T>C (p.Leu99Pro) results in a non-conservative amino acid change in the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.00024 in 251224 control chromosomes, predominantly at a frequency of 0.0034 within the African or African-American subpopulation in the gnomAD database. c.296T>C has been reported in the literature in multiple individuals affected with Vitamin D Hydroxylation-Deficient Rickets, Type 1B and has been shown to segregate in multiple families (Cheng_2004, Thacher_2015, Molin_2017). These data indicate that the variant is very likely to be associated with disease. In vitro studies have shown the variant to abolish enzyme activity (Cheng_2004, Thacher_2015, Molin_2017). Three clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as pathogenic/likely pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. -

Nov 14, 2023

Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

ACMG classification criteria: PS3 supporting, PM3 moderate, PP1 moderate, PP3 supporting -

not provided Pathogenic:2

Jan 16, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change replaces leucine, which is neutral and non-polar, with proline, which is neutral and non-polar, at codon 99 of the CYP2R1 protein (p.Leu99Pro). This variant is present in population databases (rs61495246, gnomAD 0.4%). This missense change has been observed in individuals with rickets (PMID: 15128933, 25942481, 28548312). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 2134). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. Experimental studies have shown that this missense change affects CYP2R1 function (PMID: 15128933, 25942481). For these reasons, this variant has been classified as Pathogenic. -

Aug 17, 2022

GeneDx

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Published functional studies demonstrate absent enzyme activity (Cheng et al., 2004; Thacher et al., 2015); 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: 34944511, 35739987, 25942481, 15128933, 22855339, 25003556, 15465040, 18511070, 24497297, 23548573, 8201479, 10969262, 32344004, 31841498, 30777056, 32430692, 33715104, 32596195, 27473561, 28716760, 34199067, 28548312, 32115644, 31589614, 33626316, 35973571, 34137732) -

CYP2R1-related disorder Pathogenic:1

Mar 06, 2024

PreventionGenetics, part of Exact Sciences

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

The CYP2R1 c.296T>C variant is predicted to result in the amino acid substitution p.Leu99Pro. This variant has been reported in the homozygous state in at least three families with Rickets (Cheng et al. 2004. PubMed ID: 15128933; Thacher et al. 2015. PubMed ID: 25942481; Molin et al. 2017. PubMed ID: 28548312). Additionally, functional studies indicate the p.Leu99Pro variant leads to the loss of vitamin D 25-hydroxylase enzyme activity (Cheng et al. 2004. PubMed ID: 15128933; Thacher et al. 2015. PubMed ID: 25942481). Based on the available evidence, we consider the CYP2R1 c.296T>C (p.Leu99Pro) variant to be pathogenic. -

Vitamin D-dependent rickets, type 1 Pathogenic:1

Jan 08, 2024

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The p.Leu99Pro variant in CYP2R1 has been reported in the homozygous state in 3 individuals (2 Nigerian and 1 Moroccan) with vitamin D-dependent rickets due to a disorder in vitamin D metabolism (Cheng 2004 PMID: 15128933, Thacher 2015 PMID: 25942481, Molin 2017 PMID: 28548312). One of these individuals belonged to a consanguineous family from at least 2 successive generations (Molin 2017 PMID: 28548312). The p.Leu99Pro variant also segregated with disease in 7 affected relatives from 2 families, 5 of whom were from the consanguineous family (Thacher 2015 PMID: 25942481, Molin 2017 PMID: 28548312). This variant has also been reported in the heterozygous state in one family with vitamin D-dependent rickets, where it segregated with disease in 2 affected relatives (Thacher 2015 PMID: 25942481). Affected heterozygotes in this family had milder symptoms suggesting that while vitamin D-dependent rickets is primarily an autosomal recessive disease, it has characteristics of semi dominant inheritance in this family. This variant has also been reported by other clinical laboratories in ClinVar (Variation ID: 2134) and has been identified in 0.37% (154/41454) of African chromosomes by gnomAD (http://gnomad.broadinstitute.org, v.3.1.2). Its increased frequency suggests that this may be a founder variant in this population, where the prevalence of rickets is relatively higher (Harris 2006 PMID: 16549493). In vitro functional studies provide some evidence that this variant impacts protein function (Cheng 2004 PMID: 15128933, Thacher 2015 PMID: 25942481, Molin 2017 PMID: 28548312, Casella 2020 PMID: 32115644) and computational prediction tools and conservation analyses are consistent with pathogenicity. In summary, although additional studies are required to fully establish its clinical significance, this variant meets criteria to be classified as likely pathogenic for autosomal recessive vitamin D-dependent rickets. ACMG/AMP Criteria applied: PP1_Moderate, PS3_Moderate, PM3, PP3. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.98
BayesDel_addAF	Uncertain	0.095	D
BayesDel_noAF	Pathogenic	0.36
CADD	Pathogenic	29
DANN	Pathogenic	1.0
DEOGEN2	Uncertain	0.58	D
Eigen	Pathogenic	1.1
Eigen_PC	Pathogenic	1.0
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Benign	0.84	T
M_CAP	Uncertain	0.18	D
MetaRNN	Benign	0.096	T
MetaSVM	Uncertain	0.73	D
MutationAssessor	Pathogenic	3.8	H
PhyloP100		9.3
PrimateAI	Uncertain	0.76	T
PROVEAN	Pathogenic	-5.7	D
REVEL	Pathogenic	0.78
Sift	Uncertain	0.0010	D
Sift4G	Pathogenic	0.0010	D
Polyphen		1.0	D
Vest4		0.98
MVP		0.95
MPC		0.82
ClinPred		0.26	T
GERP RS		6.2
Varity_R		0.99
gMVP		0.97
Mutation Taster		=0/100	disease causing (ClinVar)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs61495246; hg19: chr11-14907393;