chr3-149186167-ATGAAAAGTTTAGGTGCAGAATATTTATGGGAGTCATTCCCCTTCTAGTCTGATTTTCCAGCTATCTTTAAAAGGACCATAATCTAAAAAGGGATCATCTTGAGGAGCCTATGGAAGTGGAGAAAACCACACCATGTTCTTTTACTCCACATTGTCCTCAGTAACTAGGAAACAGACCTATCTGGTACATACTTCAGCTGATAGTGGCCTAGACTTGCTCTTTCAAAGATAGGAAGGGCACTTCAGAGGCTTGGGGAAGGGATAAGTTTATCACCCAACACATTCTGCTACAGGATTTTAAACCAAAACTACACAAATCCATCCAATAGAGACTTGGCTTTAAGTAAATATACCCTCTGTGTCAGGCCACATGTGGAGCGTAAGACTTGTTTGAGGGAAGAGGTTTGCTGTGTCTCTCCGTTCTCCTCTCCACAGATATGTGTTTCCTGAAAAGTATATTCCATGTACATCGGCCTCATTTCCGGCGCTGAATAAGTACCACACGACCGAATCTCCTTTGCACATAGTGAGACCCGGCTGATTCCCATACATGAATCCATTCATGGCTGTAAAAGTTGGGAAATAACATTTTGGAAGTGGTTTAGATTCTACTACATGACAACCTCACAGACTTTCCAGGACCAACTTTGTTTTTTTAATTTTTAAAAGACCTATTCAGGCTTGCCCACGCTTTATGTGTCAGGAGTATCCTTGCAACTCCTTGTGGTTCCTGGCATTTCAGAGCAGCCGCTGGCTGAAAGGAGCAGAGCTGAATGCATAGTTCTTGTTCTATGCTAGTGTCCCTAGCAACCTGGGAATCCCACTGCTCTTCCTGGCTAAAACAATGATTCTGTTAT-A
Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PVS1_ModeratePM2PP5
The NM_000096.4(CP):c.1865-291_2077+352del variant causes a splice acceptor, splice donor, splice donor 5th base, coding sequence, 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 splice_acceptor, splice_donor, splice_donor_5th_base, coding_sequence, intron
NM_000096.4 splice_acceptor, splice_donor, splice_donor_5th_base, coding_sequence, intron
Scores
Not classified
Clinical Significance
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]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 5 ACMG points.
PVS1
Splicing variant, NOT destroyed by nmd, known LOF gene, truncates exone, which is 0.06629143 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CP | NM_000096.4 | c.1865-291_2077+352del | splice_acceptor_variant, splice_donor_variant, splice_donor_5th_base_variant, coding_sequence_variant, intron_variant | 11/19 | ENST00000264613.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CP | ENST00000264613.11 | c.1865-291_2077+352del | splice_acceptor_variant, splice_donor_variant, splice_donor_5th_base_variant, coding_sequence_variant, intron_variant | 11/19 | 1 | NM_000096.4 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Deficiency of ferroxidase Pathogenic:1
Pathogenic, no assertion criteria provided | clinical testing | Dept of Medicine and Surgery, University of Milano-Bicocca | Jan 12, 2015 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at