rs6068812

Positions:

• chr20-54158096-A-G

Variant summary

Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PP5_Very_Strong

The ENST00000216862.8(CYP24A1):​c.1226T>C​(p.Leu409Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00174 in 1,613,914 control chromosomes in the GnomAD database, including 4 homozygotes. Variant has been reported in ClinVar as Likely pathogenic (★★).

• Frequency:
  • Genomes: 𝑓 0.00079 (0 hom., cov: 33)
  • Exomes 𝑓: 0.0018 (4 hom.)
• Consequence: CYP24A1 ENST00000216862.8 missense
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:10
• Conservation: PhyloP100: 8.62

Genes affected

CYP24A1 (HGNC:2602): (cytochrome P450 family 24 subfamily A 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 mitochondrial protein initiates the degradation of 1,25-dihydroxyvitamin D3, the physiologically active form of vitamin D3, by hydroxylation of the side chain. In regulating the level of vitamin D3, this enzyme plays a role in calcium homeostasis and the vitamin D endocrine system. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Likely_pathogenic. Variant got 8 ACMG points.

• PP5: Variant 20-54158096-A-G is Pathogenic according to our data. Variant chr20-54158096-A-G is described in ClinVar as [Likely_pathogenic]. Clinvar id is 29680.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr20-54158096-A-G is described in Lovd as [Likely_pathogenic]. Variant chr20-54158096-A-G is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CYP24A1	NM_000782.5	c.1226T>C	p.Leu409Ser	missense_variant	9/12	ENST00000216862.8	NP_000773.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CYP24A1	ENST00000216862.8	c.1226T>C	p.Leu409Ser	missense_variant	9/12	1	NM_000782.5	ENSP00000216862	P1
CYP24A1	ENST00000395955.7	c.1226T>C	p.Leu409Ser	missense_variant	9/11	1		ENSP00000379285
CYP24A1	ENST00000395954.3	c.800T>C	p.Leu267Ser	missense_variant	7/10	1		ENSP00000379284

Frequencies

GnomAD3 genomes AF: 0.000788 AC: 120 AN: 152252 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.000362

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000327

Gnomad ASJ AF: 0.000576

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00143

Gnomad OTH AF: 0.000478

GnomAD3 exomes AF: 0.000749 AC: 188 AN: 251066 Hom.: 0 AF XY: 0.000781 AC XY: 106 AN XY: 135718

Gnomad AFR exome AF: 0.000308

Gnomad AMR exome AF: 0.000549

Gnomad ASJ exome AF: 0.000695

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.0000327

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00135

Gnomad OTH exome AF: 0.000490

GnomAD4 exome AF: 0.00184 AC: 2696 AN: 1461544 Hom.: 4 Cov.: 32 AF XY: 0.00178 AC XY: 1297 AN XY: 727076

Gnomad4 AFR exome AF: 0.000358

Gnomad4 AMR exome AF: 0.000514

Gnomad4 ASJ exome AF: 0.000536

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000812

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00231

Gnomad4 OTH exome AF: 0.00111

GnomAD4 genome AF: 0.000788 AC: 120 AN: 152370 Hom.: 0 Cov.: 33 AF XY: 0.000725 AC XY: 54 AN XY: 74514

Gnomad4 AFR AF: 0.000361

Gnomad4 AMR AF: 0.000327

Gnomad4 ASJ AF: 0.000576

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00143

Gnomad4 OTH AF: 0.000473

Alfa AF: 0.00127 Hom.: 2

Bravo AF: 0.000858

TwinsUK AF: 0.000809 AC: 3

ALSPAC AF: 0.00285 AC: 11

ESP6500AA AF: 0.000681 AC: 3

ESP6500EA AF: 0.00163 AC: 14

ExAC AF: 0.000708 AC: 86

EpiCase AF: 0.00185

EpiControl AF: 0.00142

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:10

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Hypercalcemia, infantile, 1 Pathogenic:6

Likely pathogenic, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Sep 05, 2024	- -
Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Nov 25, 2022	Variant summary: CYP24A1 c.1226T>C (p.Leu409Ser) 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 0.00075 in 251066 control chromosomes. This frequency does not allow conclusions about variant significance. c.1226T>C has been reported in the literature in multiple individuals affected with features of Hypercalcemia, Infantile type 1, Hypercalciuric Nephrolithiasis and Nephrocalcinosis, including one case of apparent homozygosity due to UPD(20)mat leading to infantile hypercalcemia (example, Schlingmann_2011, Dinour_2013, Mugg_2015, Hureaux_2021). These data indicate that the variant is very likely to be associated with disease. At least two publications report experimental evidence evaluating an impact on protein function (example, Schlingmann_2011 and Mugg_2015). The most pronounced variant effect results in <10-30% of normal CYP24A1 enzyme activity. Six clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation (Pathogenic/Likely pathogenic, n=5; VUS, n=1). Based on the evidence outlined above, the variant was classified as pathogenic. -
Pathogenic, no assertion criteria provided	literature only	OMIM	Nov 03, 2011	- -
Pathogenic, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Jun 24, 2022	- -
Likely pathogenic, criteria provided, single submitter	research	Duke University Health System Sequencing Clinic, Duke University Health System	Apr 20, 2023	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Knight Diagnostic Laboratories, Oregon Health and Sciences University	Jul 08, 2019	- -

not provided Pathogenic:3

Likely pathogenic, criteria provided, single submitter	clinical testing	Molecular Diagnostics Lab, Nemours Children's Health, Delaware	Oct 14, 2016	- -
Pathogenic, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 29, 2024	This sequence change replaces leucine, which is neutral and non-polar, with serine, which is neutral and polar, at codon 409 of the CYP24A1 protein (p.Leu409Ser). This variant is present in population databases (rs6068812, gnomAD 0.1%), and has an allele count higher than expected for a pathogenic variant. This missense change has been observed in individual(s) with hypercalcemia and/or nephrolithiasis (PMID: 21675912, 23470222, 26214117, 26846157). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 29680). 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 CYP24A1 protein function. Experimental studies have shown that this missense change affects CYP24A1 function (PMID: 21675912, 23423976). For these reasons, this variant has been classified as Pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Jul 01, 2021	- -

CYP24A1-related disorder Pathogenic:1

Pathogenic, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Sep 19, 2024

The CYP24A1 c.1226T>C variant is predicted to result in the amino acid substitution p.Leu409Ser. This variant has been reported as causative in the homozygous and compound heterozygous states in many individuals with autosomal recessive hypercalcaemia (Schlingmann et al. 2011. PubMed ID: 21675912; Mugg et al. 2015. PubMed ID: 25375986; Gahl WA et al 2016. PubMed ID: 26846157; Hanna C et al 2021. PubMed ID: 34307984). Functional studies indicate this variant has only ~32% of wild-type activity (Jacobs ET et al 2013. PubMed ID: 23423976; Mugg et al. 2015. PubMed ID: 25375986). This variant is reported in 0.13% of alleles in individuals of European (Non-Finnish) descent in gnomAD. This variant is interpreted as pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.90
BayesDel_addAF	Uncertain	0.052	T
BayesDel_noAF	Pathogenic	0.30
CADD	Pathogenic	29
DANN	Uncertain	1.0
DEOGEN2	Uncertain	0.79	D;.;.
Eigen	Pathogenic	0.86
Eigen_PC	Pathogenic	0.80
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Uncertain	0.89	D;T;D
M_CAP	Uncertain	0.27	D
MetaRNN	Uncertain	0.47	T;T;T
MetaSVM	Uncertain	0.58	D
MutationAssessor	Uncertain	2.1	M;M;.
MutationTaster	Benign	1.0	D;D;D
PrimateAI	Uncertain	0.62	T
PROVEAN	Uncertain	-3.7	D;D;D
REVEL	Uncertain	0.52
Sift	Uncertain	0.0010	D;D;D
Sift4G	Uncertain	0.0020	D;D;D
Polyphen		1.0	D;.;.
Vest4		0.93
MVP		0.97
MPC		0.44
ClinPred		0.10	T
GERP RS		5.3
Varity_R		0.93
gMVP		0.96

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

Publications

LitVar

Other links and lift over

dbSNP: rs6068812; hg19: chr20-52774635;