2-218814186-C-T

Variant summary

Our verdict is Pathogenic. Variant got 15 ACMG points: 15P and 0B. PM1 PM2 PM5 PP3 PP5_Very_Strong

The NM_000784.4(CYP27A1):c.1183C>T(p.Arg395Cys) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000424 in 1,614,044 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 13/23 in silico tools predict a damaging outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R395S) has been classified as Likely pathogenic.

• Frequency:
  • Genomes: 𝑓 0.00029 (0 hom., cov: 32)
  • Exomes 𝑓: 0.00044 (0 hom.)
• Consequence: CYP27A1 NM_000784.4 missense, splice_region
• Scores: Splicing: ADA: 0.9911
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:21 U:1 O:1
• Conservation: PhyloP100: 1.02

Genes affected

CYP27A1 (HGNC:2605): (cytochrome P450 family 27 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 oxidizes cholesterol intermediates as part of the bile synthesis pathway. Since the conversion of cholesterol to bile acids is the major route for removing cholesterol from the body, this protein is important for overall cholesterol homeostasis. Mutations in this gene cause cerebrotendinous xanthomatosis, a rare autosomal recessive lipid storage disease. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Pathogenic. Variant got 15 ACMG points.

• PM1: In a hotspot region, there are 3 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 0 benign, 8 uncertain in NM_000784.4
• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr2-218814187-G-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 65834.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• PP3: Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: dbscSNV1_ADA, dbscSNV1_RF. No scorers claiming Uncertain. Scorers claiming Benign: max_spliceai.
• PP5: Variant 2-218814186-C-T is Pathogenic according to our data. Variant chr2-218814186-C-T is described in ClinVar as [Likely_pathogenic]. Clinvar id is 4255.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-218814186-C-T is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CYP27A1	NM_000784.4	c.1183C>T	p.Arg395Cys	missense_variant, splice_region_variant	6/9	ENST00000258415.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CYP27A1	ENST00000258415.9	c.1183C>T	p.Arg395Cys	missense_variant, splice_region_variant	6/9	1	NM_000784.4	P1
CYP27A1	ENST00000494263.5	n.1617C>T		non_coding_transcript_exon_variant	6/7	2

Frequencies

GnomAD3 genomes AF: 0.000289 AC: 44 AN: 152188 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.0000724

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000196

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000565

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000470

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.000287 AC: 72 AN: 251236 Hom.: 0 AF XY: 0.000228 AC XY: 31 AN XY: 135802

Gnomad AFR exome AF: 0.0000616

Gnomad AMR exome AF: 0.000520

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.0000980

Gnomad FIN exome AF: 0.000277

Gnomad NFE exome AF: 0.000370

Gnomad OTH exome AF: 0.000326

GnomAD4 exome AF: 0.000438 AC: 640 AN: 1461856 Hom.: 0 Cov.: 31 AF XY: 0.000418 AC XY: 304 AN XY: 727230

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.000604

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000696

Gnomad4 FIN exome AF: 0.000169

Gnomad4 NFE exome AF: 0.000528

Gnomad4 OTH exome AF: 0.000182

GnomAD4 genome AF: 0.000289 AC: 44 AN: 152188 Hom.: 0 Cov.: 32 AF XY: 0.000309 AC XY: 23 AN XY: 74346

Gnomad4 AFR AF: 0.0000724

Gnomad4 AMR AF: 0.000196

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.000565

Gnomad4 NFE AF: 0.000470

Gnomad4 OTH AF: 0.00

Alfa AF: 0.000339 Hom.: 0

Bravo AF: 0.000246

TwinsUK AF: 0.00 AC: 0

ALSPAC AF: 0.000259 AC: 1

ESP6500AA AF: 0.00 AC: 0

ESP6500EA AF: 0.000116 AC: 1

ExAC AF: 0.000173 AC: 21

EpiCase AF: 0.000382

EpiControl AF: 0.000415

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:21 Uncertain:1 Other:1

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Cholestanol storage disease Pathogenic:12 Other:1

Pathogenic, criteria provided, single submitter	research	Unidad de Genómica Médica UC, Pontificia Universidad Católica de Chile	Apr 07, 2014	This patient is a compound heterozygote for the substitution c.256-1G>T that causes exon 2 skipping, leading to a premature stop codon in exon 3, and for the pathogenic mutation c.1183C>T(p.Arg395Cys). -
Pathogenic, criteria provided, single submitter	clinical testing	Baylor Genetics	Nov 11, 2022	- -
Pathogenic, no assertion criteria provided	literature only	OMIM	Apr 25, 1991	- -
Pathogenic, criteria provided, single submitter	clinical testing	Invitae	Jan 29, 2024	This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 395 of the CYP27A1 protein (p.Arg395Cys). This variant is present in population databases (rs121908096, gnomAD 0.05%). This missense change has been observed in individuals with cerebrotendinous xanthomatosis (PMID: 2019602, 10775536, 18227423, 20402754, 21645175, 21955034, 24746394, 26156051, 26906304). This variant is also known as p.Arg362Cys. ClinVar contains an entry for this variant (Variation ID: 4255). 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 CYP27A1 function (PMID: 2019602). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. This variant disrupts the p.Arg395 amino acid residue in CYP27A1. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 8950197, 9790667). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	Dec 08, 2017	- -
Pathogenic, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Apr 28, 2017	Across a selection of the available literature, the CYP27A1 c.1183C>T (p.Arg395Cys) variant has been reported in nine studies in which is found in a total of 20 individuals with cerebrotendinous xanthomatosis, including four in a homozygous state and 16 in a compound heterozygous state, and in at least 18 additional disease alleles of unknown zygosity (Cali et al. 1991; Verrips et al. 2000; Szlago et al. 2008; Pilo-de-la-Fuente et al. 2011; Lionnet et al. 2014; Smally et al. 2015; Varman et al. 2016; Huidekoper et al. 2016; Koopal et al. 2016). The p.Arg395Cys variant was absent from 310 control alleles but is reported at a frequency of 0.00021 in the European (non-Finnish) population of the Exome Aggregation Consortium. Functional studies by Cali et al. (1991) showed the p.Arg395Cys variant had no detectable sterol 27-hydroxylase enzyme activity when expressed in COS-M6 cells. Gupta et al. (2007) demonstrated in COS-1 cells that the variant resulted in lower levels of protein expression and disrupted the heme-binding domain, resulting in an inactive protein. Based on the collective evidence, the p.Arg395Cys variant is classified pathogenic for cerebrotendinous xanthomatosis. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population. -
Pathogenic, criteria provided, single submitter	clinical testing	Myriad Genetics, Inc.	Dec 26, 2019	NM_000784.3(CYP27A1):c.1183C>T(R395C) is classified as pathogenic in the context of cerebrotendinous xanthomatosis. Sources cited for classification include the following: PMID 2019602, 10775536, 21955034 and 21645175. Classification of NM_000784.3(CYP27A1):c.1183C>T(R395C) is based on the following criteria: This is a well-established pathogenic variant in the literature that has been observed more frequently in patients with clinical diagnoses than in healthy populations. Please note: this variant was assessed in the context of healthy population screening. -
not provided, no classification provided	literature only	GeneReviews	-	Founder variant in Israeli Druze [Falik-Zaccai et al 2008] -
Pathogenic, criteria provided, single submitter	clinical testing	New York Genome Center	Apr 30, 2021	- -
Pathogenic, criteria provided, single submitter	clinical testing	Victorian Clinical Genetics Services, Murdoch Childrens Research Institute	Feb 02, 2022	Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0102 - Loss of function is a known mechanism of disease in this gene and is associated with cerebrotendinous xanthomatosis (MIM#213700). (I) 0106 - This gene is associated with autosomal recessive disease. (I) 0200 - Variant is predicted to result in a missense amino acid change from arginine to cysteine. This variant is also in a splice region (second last coding base of exon 6), however cDNA studies have shown it does not affect splicing (PMID: 25983621). (I) 0251 - This variant is heterozygous. (I) 0304 - Variant is present in gnomAD v2 <0.01 for a recessive condition (80 heterozygotes, 0 homozygotes). (SP) 0309 - Multiple alternative amino acid changes at the same position have been observed in gnomAD (v3) (highest allele count: 14 heterozygotes, 0 homozygotes). (I) 0501 - Missense variant consistently predicted to be damaging by multiple in silico tools or highly conserved with a major amino acid change. (SP) 0600 - Variant is located in the annotated Cytochrome P450 domain (DECIPHER). (I) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. This variant has previously been reported as pathogenic, in either a homozygous or compound heterozygous state, in multiple patients with cerebrotendinous xanthomatosis (ClinVar, PMIDs: 2019602, 21645175, 28324197). (SP) 0901 - This variant has strong evidence for segregation with disease. This variant has been shown to segregate with disease in multiple families (PMIDs: 21645175, 28324197). (SP) 1002 - This variant has moderate functional evidence supporting abnormal protein function. Transfected cells displayed reduced enzyme activity (PMID: 2019602). (SP) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign -
Pathogenic, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Sep 05, 2023	- -
Pathogenic, criteria provided, single submitter	clinical testing	Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein	Jul 12, 2022	ACMG classification criteria: PS3 supporting, PS4 strong, PM3 strong, PP3 supporting -
Pathogenic, no assertion criteria provided	clinical testing	Natera, Inc.	Sep 16, 2020	- -

not provided Pathogenic:8

Pathogenic, no assertion criteria provided	clinical testing	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	-	- -
Pathogenic, no assertion criteria provided	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Jun 21, 2018	- -
Pathogenic, no assertion criteria provided	clinical testing	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen	Oct 23, 2020	- -
Pathogenic, criteria provided, single submitter	clinical testing	Mayo Clinic Laboratories, Mayo Clinic	May 12, 2023	PP3, PM3_strong, PS3, PS4_moderate -
Pathogenic, no assertion criteria provided	clinical testing	Clinical Genetics, Academic Medical Center	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Apr 18, 2022	Published functional studies demonstrate a damaging effect; specifically, in vitro functional studies showed no detectable enzyme activity in cells transfected with R362C cDNA (Cali et al., 1991); Known as R362C according to alternate nomenclature; This variant is associated with the following publications: (PMID: 17697869, 10775536, 10430841, 26906304, 25983621, 12933951, 20402754, no PMID, 2019602, 8931710, 11181744, 21645175, 26156051, 21955034, 24746394, 22849591, 18227423, 28894950, 29260356, 31859899, 31980526, 33659184, 34103343, 34426522, 31589614, 33977023) -

CYP27A1-related disorder Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Feb 12, 2024

The CYP27A1 c.1183C>T variant is predicted to result in the amino acid substitution p.Arg395Cys. This variant is located within the cytochrome P-450 domain of the protein and has been reported to be causative for autosomal recessive cerebrotendinous xanthomatosis (see for examples Cali et al. 1991. PubMed ID: 2019602 [reported as p.Arg362Cys]; Smalley et al. 2015. PubMed ID: 25983621; Huidekoper et al. 2016. PubMed ID: 26156051). The Cali et al. study also performed a functional assay using transfected mammalian cell cultures that showed the p.Arg395Cys substitution greatly reduced enzymatic activity of the protein (Cali et al. 1991. PubMed ID: 2019602). This variant is reported in 0.051% of alleles in individuals of Latino descent in gnomAD. This variant has been interpreted as pathogenic by multiple independent submitters to the ClinVar database (https://www.ncbi.nlm.nih.gov/clinvar/variation/4255). Given all the evidence, we too interpret c.1183C>T (p.Arg395Cys) as pathogenic. -

Intellectual disability Uncertain:1

Uncertain significance, no assertion criteria provided

clinical testing

Centre de Biologie Pathologie Génétique, Centre Hospitalier Universitaire de Lille

Jan 01, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.77
BayesDel_addAF	Pathogenic	0.29	D
BayesDel_noAF	Pathogenic	0.53
Cadd	Pathogenic	34
Dann	Pathogenic	1.0
DEOGEN2	Pathogenic	0.87	D
Eigen	Pathogenic	0.75
Eigen_PC	Uncertain	0.64
FATHMM_MKL	Benign	0.69	D
LIST_S2	Uncertain	0.96	D
M_CAP	Pathogenic	0.54	D
MetaRNN	Pathogenic	0.98	D
MetaSVM	Pathogenic	1.1	D
MutationAssessor	Pathogenic	3.5	H
MutationTaster	Benign	1.0	D
PrimateAI	Uncertain	0.59	T
PROVEAN	Pathogenic	-7.5	D
REVEL	Pathogenic	0.91
Sift	Uncertain	0.0010	D
Sift4G	Pathogenic	0.0010	D
Polyphen		1.0	D
Vest4		0.94
MVP		0.98
MPC		0.84
ClinPred		0.60	D
GERP RS		5.8
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.98
gMVP		0.97

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	0.99
dbscSNV1_RF	Pathogenic	0.77
SpliceAI score (max)		0.12		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: rs121908096; hg19: chr2-219678909;