GeneBe

rs782299900

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_006579.3(EBP):​c.-52_-43delTTTTTTTTTT variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000129 in 772,732 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 0)
Exomes 𝑓: 0.0000013 ( 0 hom. 0 hem. )

Consequence

EBP
NM_006579.3 5_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.13

Publications

0 publications found
Variant links:
Genes affected
EBP (HGNC:3133): (EBP cholestenol delta-isomerase) The protein encoded by this gene is an integral membrane protein of the endoplasmic reticulum. It is a high affinity binding protein for the antiischemic phenylalkylamine Ca2+ antagonist [3H]emopamil and the photoaffinity label [3H]azidopamil. It is similar to sigma receptors and may be a member of a superfamily of high affinity drug-binding proteins in the endoplasmic reticulum of different tissues. This protein shares structural features with bacterial and eukaryontic drug transporting proteins. It has four putative transmembrane segments and contains two conserved glutamate residues which may be involved in the transport of cationic amphiphilics. Another prominent feature of this protein is its high content of aromatic amino acid residues (>23%) in its transmembrane segments. These aromatic amino acid residues have been suggested to be involved in the drug transport by the P-glycoprotein. Mutations in this gene cause Chondrodysplasia punctata 2 (CDPX2; also known as Conradi-Hunermann syndrome). [provided by RefSeq, Jul 2008]
EBP Gene-Disease associations (from GenCC):
  • chondrodysplasia punctata 2, X-linked dominant
    Inheritance: XL Classification: DEFINITIVE Submitted by: Illumina
  • MEND syndrome
    Inheritance: XL Classification: DEFINITIVE, STRONG, MODERATE, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Orphanet, Genomics England PanelApp, ClinGen
  • X-linked chondrodysplasia punctata 2
    Inheritance: XL Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Orphanet, G2P

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006579.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
EBP
NM_006579.3
MANE Select
c.-52_-43delTTTTTTTTTT
5_prime_UTR
Exon 2 of 5NP_006570.1Q15125

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
EBP
ENST00000495186.6
TSL:1 MANE Select
c.-52_-43delTTTTTTTTTT
5_prime_UTR
Exon 2 of 5ENSP00000417052.1Q15125
ENSG00000286268
ENST00000651615.1
c.-52_-43delTTTTTTTTTT
5_prime_UTR
Exon 2 of 7ENSP00000498524.1A0A494C0F3
EBP
ENST00000882075.1
c.-52_-43delTTTTTTTTTT
5_prime_UTR
Exon 3 of 6ENSP00000552134.1

Frequencies

GnomAD3 genomes
Cov.:
0
GnomAD4 exome
AF:
0.00000129
AC:
1
AN:
772732
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
226002
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
18219
American (AMR)
AF:
0.00
AC:
0
AN:
19998
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
15663
East Asian (EAS)
AF:
0.00
AC:
0
AN:
24400
South Asian (SAS)
AF:
0.00
AC:
0
AN:
38888
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
31147
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
2292
European-Non Finnish (NFE)
AF:
0.00000170
AC:
1
AN:
587747
Other (OTH)
AF:
0.00
AC:
0
AN:
34378
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.625
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
Cov.:
0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
PhyloP100
1.1

Splicing

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

Publications

Other links and lift over

dbSNP: rs782299900; hg19: chrX-48382099; API