rs1553759167

Variant names:

• chr3-149185282-GTGGGGAATAATCCCATTCCACCTCCACTGCTGCGATATAGTATGTCCTCTCTCCCAGGTAGAAGGTGGAATCCTCAGACTGCCGCCTGCATTGGTTCACAGTATATTTTTGCTTCATGCCGCCTGTGTAATGATCAGTTGTAAGGCATTCAACATTAAAAGTCCCTGGAGTGGTAAATAAGAAAACATGTCACTTCTTTGCTAGTGCCCTCTGGGGCTCTCCACCTTCCTCAGAATTA-G
• rs1553759167
• NM_000096.4:c.2078-74_2241del

Variant summary

Our verdict is Likely pathogenic. The variant received 9 ACMG points: 9P and 0B. PVS1 PP5

The NM_000096.4(CP):​c.2078-74_2241del​(p.Gly693fs) variant causes a frameshift, splice acceptor, splice region, intron change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. Variant has been reported in ClinVar as Pathogenic (no stars). Variant results in nonsense mediated mRNA decay.

• Frequency: Genomes: not found (cov: 32)
• Consequence: CP NM_000096.4 frameshift, splice_acceptor, splice_region, intron
• Clinical Significance: Pathogenic no assertion criteria provided P:1
• Conservation: PhyloP100: 9.13
• Publications: 0 publications found

Genes affected

CP (HGNC:2295): (ceruloplasmin) The protein encoded by this gene is a metalloprotein that binds most of the copper in plasma and is involved in the peroxidation of Fe(II)transferrin to Fe(III) transferrin. Mutations in this gene cause aceruloplasminemia, which results in iron accumulation and tissue damage, and is associated with diabetes and neurologic abnormalities. Two transcript variants, one protein-coding and the other not protein-coding, have been found for this gene. [provided by RefSeq, Feb 2012]

CP Gene-Disease associations (from GenCC):

• aceruloplasminemia

  Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Genomics England PanelApp, Orphanet, Labcorp Genetics (formerly Invitae), Ambry Genetics
• disorder of iron metabolism and transport

  Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics

ACMG classification

Our verdict: Likely_pathogenic. The variant received 9 ACMG points.

• PVS1: Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
• PP5: Variant 3-149185282-GTGGGGAATAATCCCATTCCACCTCCACTGCTGCGATATAGTATGTCCTCTCTCCCAGGTAGAAGGTGGAATCCTCAGACTGCCGCCTGCATTGGTTCACAGTATATTTTTGCTTCATGCCGCCTGTGTAATGATCAGTTGTAAGGCATTCAACATTAAAAGTCCCTGGAGTGGTAAATAAGAAAACATGTCACTTCTTTGCTAGTGCCCTCTGGGGCTCTCCACCTTCCTCAGAATTA-G is Pathogenic according to our data. Variant chr3-149185282-GTGGGGAATAATCCCATTCCACCTCCACTGCTGCGATATAGTATGTCCTCTCTCCCAGGTAGAAGGTGGAATCCTCAGACTGCCGCCTGCATTGGTTCACAGTATATTTTTGCTTCATGCCGCCTGTGTAATGATCAGTTGTAAGGCATTCAACATTAAAAGTCCCTGGAGTGGTAAATAAGAAAACATGTCACTTCTTTGCTAGTGCCCTCTGGGGCTCTCCACCTTCCTCAGAATTA-G is described in ClinVar as Pathogenic. ClinVar VariationId is 488149.Status of the report is no_assertion_criteria_provided, 0 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CP	NM_000096.4	c.2078-74_2241del	p.Gly693fs	frameshift_variant, splice_acceptor_variant, splice_region_variant, intron_variant	Exon 12 of 19	ENST00000264613.11	NP_000087.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CP	ENST00000264613.11	c.2078-74_2241del	p.Gly693fs	frameshift_variant, splice_acceptor_variant, splice_region_variant, intron_variant	Exon 12 of 19	1	NM_000096.4	ENSP00000264613.6

Frequencies

GnomAD3 genomes Cov.: 32

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: no assertion criteria provided

Submissions by phenotype

Deficiency of ferroxidase Pathogenic:1

Jan 14, 2015

Dept of Medicine and Surgery, University of Milano-Bicocca

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		9.1
Mutation Taster		=3/197	disease causing (ClinVar)

Splicing

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

Other links and lift over

dbSNP: rs1553759167; hg19: chr3-148903069;