rs1554998040
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PVS1PM2PP5
The NM_145200.5(CABP4):c.800-18_*795del variant causes a splice acceptor, coding sequence, 3 prime UTR, 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 Likely pathogenic (no stars).
Frequency
Genomes: not found (cov: 32)
Consequence
CABP4
NM_145200.5 splice_acceptor, coding_sequence, 3_prime_UTR, intron
NM_145200.5 splice_acceptor, coding_sequence, 3_prime_UTR, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.672
Genes affected
CABP4 (HGNC:1386): (calcium binding protein 4) This gene encodes a member of the CABP family of calcium binding protein characterized by four EF-hand motifs. Mutations in this gene are associated with congenital stationary night blindness type 2B. Three transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, Jul 2014]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 11 ACMG points.
PVS1
Splicing +-2 bp (donor or acceptor) variant, LoF is a know mechanism of disease, No cryptic splice site detected. Exon removal results in frameshift change.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 11-67458612-CTGCCCTTCTCTCCCGCAGAGTTTGTGATGATGCTCTCCCGCCACTGAGGCTCCAGGAGGGAATATCTGTTGCCCCTGCGGCCCCAGACACCAGCCAGACCCAGGCTGCAGGCCTCCCCCAGGAGCCTCCAGGATGGAGATGGAGACCCAGCAGCCCCCAGACTACTTCTATCCCTGAAAACACCTGGCCTCAATGTTGGCTTGTTATGTTACCTGCCCACCCTCATCCTTACCTCCTCCTACTCAAGCTGCCTGGAGAAGACCTGCTCTCAGCTGCCCACCGTTCCTCAGTGTGAGCAAGATTTGGGTCTCTCCAGACCTCTGGGAGGTAGGGAGTTCCCTGGCACTGGCAGCATTCAGTGGGGACCCCCCAGTGGCATGATGAATGGAGAGGATGGCTGGACCCCTTCCACTACTTATGTTTATAATTTTTTTTTTTTTTAATGAACTTGAGCCGGGTGCAGTGGCTCACACCTGTAAGCCCAGCTGTCAGGGGGCAGAAGCGGGAGGATAGCTTGAGCCCAGGAGTGCAAGACCTGCCTGGGCAATATACTGAGACCCCATTCTCCACAAAAAGGAAAAATAAAAGACAAAAAAACAAACAAAAAACCAAAAAACCCAAGTGTAAAAAAAGTGAGCTTGAAAGAAAGAAAGGGATGGCTCCATGTATCAAAGACAAAGAAATCAAAGCTGGGGTTGTAAGAGGGAGCTGACGCTGTGGGGGTTTCAGATCTGGATGGAGGCTTGGCCGCCTGGACTCCTACAACCATGAGTGACAGAAGAACCATATGAGTCTGGGGAGCAAGAAACAAACCCCCCGGATATATTCCAGGGTCTCCAAAG-C is Pathogenic according to our data. Variant chr11-67458612-CTGCCCTTCTCTCCCGCAGAGTTTGTGATGATGCTCTCCCGCCACTGAGGCTCCAGGAGGGAATATCTGTTGCCCCTGCGGCCCCAGACACCAGCCAGACCCAGGCTGCAGGCCTCCCCCAGGAGCCTCCAGGATGGAGATGGAGACCCAGCAGCCCCCAGACTACTTCTATCCCTGAAAACACCTGGCCTCAATGTTGGCTTGTTATGTTACCTGCCCACCCTCATCCTTACCTCCTCCTACTCAAGCTGCCTGGAGAAGACCTGCTCTCAGCTGCCCACCGTTCCTCAGTGTGAGCAAGATTTGGGTCTCTCCAGACCTCTGGGAGGTAGGGAGTTCCCTGGCACTGGCAGCATTCAGTGGGGACCCCCCAGTGGCATGATGAATGGAGAGGATGGCTGGACCCCTTCCACTACTTATGTTTATAATTTTTTTTTTTTTTAATGAACTTGAGCCGGGTGCAGTGGCTCACACCTGTAAGCCCAGCTGTCAGGGGGCAGAAGCGGGAGGATAGCTTGAGCCCAGGAGTGCAAGACCTGCCTGGGCAATATACTGAGACCCCATTCTCCACAAAAAGGAAAAATAAAAGACAAAAAAACAAACAAAAAACCAAAAAACCCAAGTGTAAAAAAAGTGAGCTTGAAAGAAAGAAAGGGATGGCTCCATGTATCAAAGACAAAGAAATCAAAGCTGGGGTTGTAAGAGGGAGCTGACGCTGTGGGGGTTTCAGATCTGGATGGAGGCTTGGCCGCCTGGACTCCTACAACCATGAGTGACAGAAGAACCATATGAGTCTGGGGAGCAAGAAACAAACCCCCCGGATATATTCCAGGGTCTCCAAAG-C is described in ClinVar as [Likely_pathogenic]. Clinvar id is 438232.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CABP4 | NM_145200.5 | c.800-18_*795del | splice_acceptor_variant, coding_sequence_variant, 3_prime_UTR_variant, intron_variant | 6/6 | ENST00000325656.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CABP4 | ENST00000325656.7 | c.800-18_*795del | splice_acceptor_variant, coding_sequence_variant, 3_prime_UTR_variant, intron_variant | 6/6 | 1 | NM_145200.5 | P1 | ||
CABP4 | ENST00000438189.6 | splice_acceptor_variant, coding_sequence_variant, 3_prime_UTR_variant, intron_variant | 7/7 | 1 |
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: Likely pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Retinal dystrophy Pathogenic:1
Likely pathogenic, no assertion criteria provided | research | NIHR Bioresource Rare Diseases, University of Cambridge | - | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at