NM_006579.3:c.-46_-43dupTTTT

Variant names:

• chrX-48523711-C-CTTTT
• rs782299900
• NM_006579.3:c.-46_-43dupTTTT

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BS1 BS2

The NM_006579.3(EBP):​c.-46_-43dupTTTT variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.00013 (0 hom., 3 hem., cov: 0)
  • Exomes 𝑓: 0.0025 (3 hom. 49 hem.)
• Consequence: EBP NM_006579.3 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.474
• Publications: 2 publications found

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

ENSG00000286268 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.000126 (11/87620) while in subpopulation NFE AF = 0.0002 (9/45036). AF 95% confidence interval is 0.000104. There are 0 homozygotes in GnomAd4. There are 3 alleles in the male GnomAd4 subpopulation. Median coverage is 0. This position passed quality control check.
• BS2: High Hemizygotes in GnomAd4 at 3 XL gene

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.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EBP	NM_006579.3	MANE Select	c.-46_-43dupTTTT		5_prime_UTR	Exon 2 of 5	NP_006570.1	Q15125

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EBP	ENST00000495186.6	TSL:1 MANE Select	c.-46_-43dupTTTT		5_prime_UTR	Exon 2 of 5	ENSP00000417052.1	Q15125
	ENSG00000286268	ENST00000651615.1		c.-46_-43dupTTTT		5_prime_UTR	Exon 2 of 7	ENSP00000498524.1	A0A494C0F3
	EBP	ENST00000882075.1		c.-46_-43dupTTTT		5_prime_UTR	Exon 3 of 6	ENSP00000552134.1

Frequencies

GnomAD3 genomes AF: 0.000126 AC: 11 AN: 87645 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.0000420

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.000430

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000200

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.00246 AC: 1896 AN: 769302 Hom.: 3 Cov.: 0 AF XY: 0.000218 AC XY: 49 AN XY: 224334

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.000495 AC: 9 AN: 18199

American (AMR) AF: 0.00161 AC: 32 AN: 19936

Ashkenazi Jewish (ASJ) AF: 0.00503 AC: 78 AN: 15498

East Asian (EAS) AF: 0.00 AC: 0 AN: 24391

South Asian (SAS) AF: 0.00283 AC: 109 AN: 38526

European-Finnish (FIN) AF: 0.00119 AC: 37 AN: 31054

Middle Eastern (MID) AF: 0.00845 AC: 19 AN: 2249

European-Non Finnish (NFE) AF: 0.00261 AC: 1528 AN: 585269

Other (OTH) AF: 0.00246 AC: 84 AN: 34180

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome AF: 0.000126 AC: 11 AN: 87620 Hom.: 0 Cov.: 0 AF XY: 0.000153 AC XY: 3 AN XY: 19554

African (AFR) AF: 0.0000420 AC: 1 AN: 23828

American (AMR) AF: 0.00 AC: 0 AN: 7480

Ashkenazi Jewish (ASJ) AF: 0.000430 AC: 1 AN: 2327

East Asian (EAS) AF: 0.00 AC: 0 AN: 2752

South Asian (SAS) AF: 0.00 AC: 0 AN: 1775

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2487

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 166

European-Non Finnish (NFE) AF: 0.000200 AC: 9 AN: 45036

Other (OTH) AF: 0.00 AC: 0 AN: 1165

Alfa AF: 0.00 Hom.: 352

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.47
Mutation Taster		=300/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs782299900; hg19: chrX-48382099;