rs1553759338

Variant names:

• chr3-149186167-ATGAAAAGTTTAGGTGCAGAATATTTATGGGAGTCATTCCCCTTCTAGTCTGATTTTCCAGCTATCTTTAAAAGGACCATAATCTAAAAAGGGATCATCTTGAGGAGCCTATGGAAGTGGAGAAAACCACACCATGTTCTTTTACTCCACATTGTCCTCAGTAACTAGGAAACAGACCTATCTGGTACATACTTCAGCTGATAGTGGCCTAGACTTGCTCTTTCAAAGATAGGAAGGGCACTTCAGAGGCTTGGGGAAGGGATAAGTTTATCACCCAACACATTCTGCTACAGGATTTTAAACCAAAACTACACAAATCCATCCAATAGAGACTTGGCTTTAAGTAAATATACCCTCTGTGTCAGGCCACATGTGGAGCGTAAGACTTGTTTGAGGGAAGAGGTTTGCTGTGTCTCTCCGTTCTCCTCTCCACAGATATGTGTTTCCTGAAAAGTATATTCCATGTACATCGGCCTCATTTCCGGCGCTGAATAAGTACCACACGACCGAATCTCCTTTGCACATAGTGAGACCCGGCTGATTCCCATACATGAATCCATTCATGGCTGTAAAAGTTGGGAAATAACATTTTGGAAGTGGTTTAGATTCTACTACATGACAACCTCACAGACTTTCCAGGACCAACTTTGTTTTTTTAATTTTTAAAAGACCTATTCAGGCTTGCCCACGCTTTATGTGTCAGGAGTATCCTTGCAACTCCTTGTGGTTCCTGGCATTTCAGAGCAGCCGCTGGCTGAAAGGAGCAGAGCTGAATGCATAGTTCTTGTTCTATGCTAGTGTCCCTAGCAACCTGGGAATCCCACTGCTCTTCCTGGCTAAAACAATGATTCTGTTAT-A
• rs1553759338
• NM_000096.4:c.1865-291_2077+352del

Variant summary

Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PVS1_Moderate PM2 PP5

The NM_000096.4(CP):​c.1865-291_2077+352del variant causes a exon loss, splice acceptor, splice donor, splice region, intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (no stars).

• Frequency: Genomes: not found (cov: 32)
• Consequence: CP NM_000096.4 exon_loss, splice_acceptor, splice_donor, splice_region, intron
• Clinical Significance: Pathogenic no assertion criteria provided P:1
• Conservation: PhyloP100: 1.39

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 5 ACMG points.

• PVS1: Splicing +-2 bp (donor or acceptor) variant, product NOT destroyed by NMD, known LOF gene, truncates exone, which is 0.06660413 fraction of the gene. No cryptic splice site detected. Exon removal is inframe change.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 3-149186167-ATGAAAAGTTTAGGTGCAGAATATTTATGGGAGTCATTCCCCTTCTAGTCTGATTTTCCAGCTATCTTTAAAAGGACCATAATCTAAAAAGGGATCATCTTGAGGAGCCTATGGAAGTGGAGAAAACCACACCATGTTCTTTTACTCCACATTGTCCTCAGTAACTAGGAAACAGACCTATCTGGTACATACTTCAGCTGATAGTGGCCTAGACTTGCTCTTTCAAAGATAGGAAGGGCACTTCAGAGGCTTGGGGAAGGGATAAGTTTATCACCCAACACATTCTGCTACAGGATTTTAAACCAAAACTACACAAATCCATCCAATAGAGACTTGGCTTTAAGTAAATATACCCTCTGTGTCAGGCCACATGTGGAGCGTAAGACTTGTTTGAGGGAAGAGGTTTGCTGTGTCTCTCCGTTCTCCTCTCCACAGATATGTGTTTCCTGAAAAGTATATTCCATGTACATCGGCCTCATTTCCGGCGCTGAATAAGTACCACACGACCGAATCTCCTTTGCACATAGTGAGACCCGGCTGATTCCCATACATGAATCCATTCATGGCTGTAAAAGTTGGGAAATAACATTTTGGAAGTGGTTTAGATTCTACTACATGACAACCTCACAGACTTTCCAGGACCAACTTTGTTTTTTTAATTTTTAAAAGACCTATTCAGGCTTGCCCACGCTTTATGTGTCAGGAGTATCCTTGCAACTCCTTGTGGTTCCTGGCATTTCAGAGCAGCCGCTGGCTGAAAGGAGCAGAGCTGAATGCATAGTTCTTGTTCTATGCTAGTGTCCCTAGCAACCTGGGAATCCCACTGCTCTTCCTGGCTAAAACAATGATTCTGTTAT-A is Pathogenic according to our data. Variant chr3-149186167-ATGAAAAGTTTAGGTGCAGAATATTTATGGGAGTCATTCCCCTTCTAGTCTGATTTTCCAGCTATCTTTAAAAGGACCATAATCTAAAAAGGGATCATCTTGAGGAGCCTATGGAAGTGGAGAAAACCACACCATGTTCTTTTACTCCACATTGTCCTCAGTAACTAGGAAACAGACCTATCTGGTACATACTTCAGCTGATAGTGGCCTAGACTTGCTCTTTCAAAGATAGGAAGGGCACTTCAGAGGCTTGGGGAAGGGATAAGTTTATCACCCAACACATTCTGCTACAGGATTTTAAACCAAAACTACACAAATCCATCCAATAGAGACTTGGCTTTAAGTAAATATACCCTCTGTGTCAGGCCACATGTGGAGCGTAAGACTTGTTTGAGGGAAGAGGTTTGCTGTGTCTCTCCGTTCTCCTCTCCACAGATATGTGTTTCCTGAAAAGTATATTCCATGTACATCGGCCTCATTTCCGGCGCTGAATAAGTACCACACGACCGAATCTCCTTTGCACATAGTGAGACCCGGCTGATTCCCATACATGAATCCATTCATGGCTGTAAAAGTTGGGAAATAACATTTTGGAAGTGGTTTAGATTCTACTACATGACAACCTCACAGACTTTCCAGGACCAACTTTGTTTTTTTAATTTTTAAAAGACCTATTCAGGCTTGCCCACGCTTTATGTGTCAGGAGTATCCTTGCAACTCCTTGTGGTTCCTGGCATTTCAGAGCAGCCGCTGGCTGAAAGGAGCAGAGCTGAATGCATAGTTCTTGTTCTATGCTAGTGTCCCTAGCAACCTGGGAATCCCACTGCTCTTCCTGGCTAAAACAATGATTCTGTTAT-A is described in ClinVar as [Pathogenic]. Clinvar id is 488148.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.1865-291_2077+352del		exon_loss_variant, splice_acceptor_variant, splice_donor_variant, splice_region_variant, intron_variant	Exon 11 of 19	ENST00000264613.11	NP_000087.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CP	ENST00000264613.11	c.1865-291_2077+352del		exon_loss_variant, splice_acceptor_variant, splice_donor_variant, splice_region_variant, intron_variant	Exon 11 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 12, 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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1553759338; hg19: chr3-148903954;