chr2-218814188-G-A

Position:

• chr2-218814188-G-A

Variant summary

Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1 PM2 PP5_Very_Strong

The NM_000784.4(CYP27A1):​c.1184+1G>A variant causes a splice donor change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000128 in 1,614,128 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Pathogenic (★★).

• Frequency:
  • Genomes: 𝑓 0.000092 (0 hom., cov: 32)
  • Exomes 𝑓: 0.00013 (0 hom.)
• Consequence: CYP27A1 NM_000784.4 splice_donor
• Scores: Splicing: ADA: 1.000
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:21
• Conservation: PhyloP100: 9.81

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 18 ACMG points.

• PVS1: Splicing +-2 bp (donor or acceptor) variant, LoF is a know mechanism of disease, No cryptic splice site detected. Exon removal results in frameshift change.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 2-218814188-G-A is Pathogenic according to our data. Variant chr2-218814188-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 65833.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-218814188-G-A is described in Lovd as [Pathogenic]. Variant chr2-218814188-G-A is described in Lovd as [Likely_pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CYP27A1	NM_000784.4	c.1184+1G>A		splice_donor_variant		ENST00000258415.9	NP_000775.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CYP27A1	ENST00000258415.9	c.1184+1G>A		splice_donor_variant		1	NM_000784.4	ENSP00000258415	P1
CYP27A1	ENST00000494263.5	n.1619G>A		non_coding_transcript_exon_variant	6/7	2

Frequencies

GnomAD3 genomes AF: 0.0000920 AC: 14 AN: 152254 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000414

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000176

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.000159 AC: 40 AN: 251280 Hom.: 0 AF XY: 0.000214 AC XY: 29 AN XY: 135822

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.000719

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000150

Gnomad OTH exome AF: 0.000163

GnomAD4 exome AF: 0.000132 AC: 193 AN: 1461874 Hom.: 0 Cov.: 31 AF XY: 0.000165 AC XY: 120 AN XY: 727238

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000869

Gnomad4 FIN exome AF: 0.0000187

Gnomad4 NFE exome AF: 0.0000998

Gnomad4 OTH exome AF: 0.0000828

GnomAD4 genome AF: 0.0000920 AC: 14 AN: 152254 Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8 AN XY: 74390

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000414

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000176

Gnomad4 OTH AF: 0.00

Alfa AF: 0.000141 Hom.: 0

Bravo AF: 0.0000529

ExAC AF: 0.000140 AC: 17

EpiCase AF: 0.000109

EpiControl AF: 0.0000593

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:21

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Cholestanol storage disease Pathogenic:11

Pathogenic, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 18, 2024	This sequence change affects a donor splice site in intron 6 of the CYP27A1 gene. RNA analysis indicates that disruption of this splice site induces altered splicing and may result in an absent or disrupted protein product. This variant is present in population databases (rs587778777, gnomAD 0.07%). Disruption of this splice site has been observed in individuals with cerebrotendinous xanthomatosis (PMID: 9392430, 21645175, 28894950). This variant is also known as In6+1G>A. ClinVar contains an entry for this variant (Variation ID: 65833). Studies have shown that disruption of this splice site results in skipping of 89 nucleotides of exon 6 and introduces a premature termination codon (PMID: 9392430). The resulting mRNA is expected to undergo nonsense-mediated decay. For these reasons, this variant has been classified as Pathogenic. -
Pathogenic, no assertion criteria provided	curation	GeneReviews	Aug 01, 2013	- -
Pathogenic, criteria provided, single submitter	clinical testing	Baylor Genetics	Mar 26, 2024	- -
Pathogenic, criteria provided, single submitter	clinical testing	Fulgent Genetics, Fulgent Genetics	Dec 20, 2021	- -
Pathogenic, criteria provided, single submitter	clinical testing	Neuberg Centre For Genomic Medicine, NCGM	May 20, 2023	The observed invariant splice acceptor variant c.1184+1G>A in CYP27A1 gene has been reported previously in both homozygous and compound heterozygous state in multiple inviduals affected with cerebrotendinous xanthomatosis (Ginanneschi et al. 2013; Rashvand et al. 2021). Experimental evidence shows that this variant activates a cryptic donor splice site and leads to skipping of 89 base pairs of exon 6, introduces a new reading frame and creates a premature stop codon that does not three essential amino acids (Lys354, Lys358, and Arg362) that are important for the ferredoxin-binding domain (Rashvand et al. 2021). The c.1184+1G>A variant is present with an allele frequency of 0.02% on gnomAD Exomes database. This variant has been submitted to the ClinVar database as Likely Pathogenic / Pathogenic (multiple submissions). SpliceAI predicts a splice donor loss of 0.99 for this variant. Loss of function variants in CYP27A1 gene have been previously reported to be disease causing. For these reasons, this variant has been classified as Pathogenic. In the absence of another reportable variant in the CYP27A1 gene, the molecular diagnosis is not confirmed. -
Pathogenic, criteria provided, single submitter	clinical testing	Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	May 13, 2022	Variant summary: CYP27A1 c.1184+1G>A is located in a canonical splice-site and is predicted to affect mRNA splicing resulting in a significantly altered protein due to either exon skipping, shortening, or inclusion of intronic material. Several computational tools predict a significant impact on normal splicing: Three predict the variant abolishes the canonical 5' splicing donor site. At least one publication reports experimental evidence that this variant affects mRNA splicing by skipping of exon 7 and joining exon 6 to exon 8 that translates to a sequence of 28 novel amino acids preceding a termination codon (Garuti_1996). The variant allele was found at a frequency of 0.00016 in 251280 control chromosomes. This frequency is not significantly higher than estimated for a pathogenic variant in CYP27A1 causing Cerebrotendinous Xanthomatosis (0.00016 vs 0.0011), allowing no conclusion about variant significance. c.1184+1G>A has been reported in the literature as homozygous and compound heterozygous genotypes in multiple individuals affected with Cerebrotendinous Xanthomatosis (example, Garuti_1996, Gianneschi_2013). These data indicate that the variant is very likely to be associated with disease. Eight 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. Based on the evidence outlined above, the variant was classified as pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Centogene AG - the Rare Disease Company	-	- -
Pathogenic, no assertion criteria provided	clinical testing	Natera, Inc.	Sep 16, 2020	- -
Pathogenic, criteria provided, single submitter	clinical testing	Myriad Genetics, Inc.	Oct 20, 2021	NM_000784.3(CYP27A1):c.1184+1G>A is a canonical splice variant classified as pathogenic in the context of cerebrotendinous xanthomatosis. c.1184+1G>A has been observed in cases with relevant disease (PMID: 22878431). Functional assessments of this variant are available in the literature (PMID: 9392430). c.1184+1G>A has been observed in population frequency databases (gnomAD: SAS 0.07%). In summary, NM_000784.3(CYP27A1):c.1184+1G>A is a canonical splice variant in a gene where loss of function is a known mechanism of disease, is predicted to disrupt protein function, and has been observed more frequently in cases with the relevant disease than in healthy populations. Please note: this variant was assessed in the context of healthy population screening. -
Pathogenic, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Oct 28, 2022	- -

not provided Pathogenic:8

Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	May 09, 2022	Observed in the homozygous state or with a pathogenic variant on the opposite allele (in trans) in patients with cerebrotendinous xanthomatosis referred for genetic testing at GeneDx and in published literature (Garuti et al., 1997; Verrips et al., 2000; Lee et al., 2001; Lipinski et al., 2020); Canonical splice site variant and published functional studies demonstrate that this variant leads to the production of three abnormal transcripts, and almost undetectable levels of mRNA in patient fibroblasts (Garuti et al., 1997); This variant is associated with the following publications: (PMID: 10775536, 25525159, 11181744, 26643207, 20402754, 28894950, 29260356, 32793533, 33659184, 34066437, 33400472, 31589614, 33083013, 33520900, 9392430) -
Likely pathogenic, no assertion criteria provided	clinical testing	Clinical Genetics, Academic Medical Center	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Oct 10, 2017	- -
Pathogenic, no assertion criteria provided	clinical testing	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	-	- -
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	CeGaT Center for Human Genetics Tuebingen	Dec 01, 2021	- -
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 05, 2023	PP3, PM3, PS3, PS4, PVS1 -

CYP27A1-related disorder Pathogenic:1

Pathogenic, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

May 02, 2024

The CYP27A1 c.1184+1G>A variant is predicted to disrupt the GT donor site and interfere with normal splicing. This variant has been reported in the homozygous and compound heterozygous states in individuals with cerebrotendinous xanthomatosis (see for example Garuti et al. 1997. PubMed ID: 9392430; Lipiński et al. 2020. PubMed ID: 32793533). This variant is reported in 0.072% of alleles in individuals of South Asian descent in gnomAD. Variants that disrupt the consensus splice donor site in CYP27A1 are expected to be pathogenic, and this variant has been classified as pathogenic by multiple independent submitters to the ClinVar database (https://www.ncbi.nlm.nih.gov/clinvar/variation/65833). Given all the evidence, we interpret c.1184+1G>A as pathogenic. -

Cardiovascular phenotype Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Feb 28, 2022

The c.1184+1G>A intronic alteration consists of a G to A substitution one nucleotide after coding exon 6 of the CYP27A1 gene. Alterations that disrupt the canonical splice donor site are typically deleterious in nature (Richards, 2015). Based on data from gnomAD, the A allele has an overall frequency of 0.02% (46/282682) total alleles studied. The highest observed frequency was 0.07% (22/30614) of South Asian alleles. This alteration has been detected in the homozygous state and in trans with other disease-causing CYP27A1 alterations in multiple unrelated individuals diagnosed with cerebrotendinous xanthomatosis (Stelten, 2018; Lipiski, 2020; Lipiski, 2020; Rashvand, 2021; Ginanneschi, 2013; Lee, 2001). This nucleotide position is highly conserved in available vertebrate species. Experimental studies show this alteration results in abnormal splicing and introduces a frameshift (Garuti, 1997). In silico splice site analysis predicts that this alteration will weaken the native splice donor site. Based on the available evidence, this alteration is classified as pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.37	D
BayesDel_noAF	Pathogenic	0.42
CADD	Pathogenic	33
DANN	Uncertain	1.0
Eigen	Pathogenic	1.2
Eigen_PC	Pathogenic	1.1
FATHMM_MKL	Pathogenic	0.99	D
MutationTaster	Benign	1.0	D
GERP RS		5.5
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.94
SpliceAI score (max)		0.99		Details are displayed if max score is > 0.2
DS_DL_spliceai		0.99		Position offset: -1

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

Publications

LitVar

Other links and lift over

dbSNP: rs587778777; hg19: chr2-219678911;