chr11-67458612-CTGCCCTTCTCTCCCGCAGAGTTTGTGATGATGCTCTCCCGCCACTGAGGCTCCAGGAGGGAATATCTGTTGCCCCTGCGGCCCCAGACACCAGCCAGACCCAGGCTGCAGGCCTCCCCCAGGAGCCTCCAGGATGGAGATGGAGACCCAGCAGCCCCCAGACTACTTCTATCCCTGAAAACACCTGGCCTCAATGTTGGCTTGTTATGTTACCTGCCCACCCTCATCCTTACCTCCTCCTACTCAAGCTGCCTGGAGAAGACCTGCTCTCAGCTGCCCACCGTTCCTCAGTGTGAGCAAGATTTGGGTCTCTCCAGACCTCTGGGAGGTAGGGAGTTCCCTGGCACTGGCAGCATTCAGTGGGGACCCCCCAGTGGCATGATGAATGGAGAGGATGGCTGGACCCCTTCCACTACTTATGTTTATAATTTTTTTTTTTTTTAATGAACTTGAGCCGGGTGCAGTGGCTCACACCTGTAAGCCCAGCTGTCAGGGGGCAGAAGCGGGAGGATAGCTTGAGCCCAGGAGTGCAAGACCTGCCTGGGCAATATACTGAGACCCCATTCTCCACAAAAAGGAAAAATAAAAGACAAAAAAACAAACAAAAAACCAAAAAACCCAAGTGTAAAAAAAGTGAGCTTGAAAGAAAGAAAGGGATGGCTCCATGTATCAAAGACAAAGAAATCAAAGCTGGGGTTGTAAGAGGGAGCTGACGCTGTGGGGGTTTCAGATCTGGATGGAGGCTTGGCCGCCTGGACTCCTACAACCATGAGTGACAGAAGAACCATATGAGTCTGGGGAGCAAGAAACAAACCCCCCGGATATATTCCAGGGTCTCCAAAG-C

Variant names:

• chr11-67458612-CTGCCCTTCTCTCCCGCAGAGTTTGTGATGATGCTCTCCCGCCACTGAGGCTCCAGGAGGGAATATCTGTTGCCCCTGCGGCCCCAGACACCAGCCAGACCCAGGCTGCAGGCCTCCCCCAGGAGCCTCCAGGATGGAGATGGAGACCCAGCAGCCCCCAGACTACTTCTATCCCTGAAAACACCTGGCCTCAATGTTGGCTTGTTATGTTACCTGCCCACCCTCATCCTTACCTCCTCCTACTCAAGCTGCCTGGAGAAGACCTGCTCTCAGCTGCCCACCGTTCCTCAGTGTGAGCAAGATTTGGGTCTCTCCAGACCTCTGGGAGGTAGGGAGTTCCCTGGCACTGGCAGCATTCAGTGGGGACCCCCCAGTGGCATGATGAATGGAGAGGATGGCTGGACCCCTTCCACTACTTATGTTTATAATTTTTTTTTTTTTTAATGAACTTGAGCCGGGTGCAGTGGCTCACACCTGTAAGCCCAGCTGTCAGGGGGCAGAAGCGGGAGGATAGCTTGAGCCCAGGAGTGCAAGACCTGCCTGGGCAATATACTGAGACCCCATTCTCCACAAAAAGGAAAAATAAAAGACAAAAAAACAAACAAAAAACCAAAAAACCCAAGTGTAAAAAAAGTGAGCTTGAAAGAAAGAAAGGGATGGCTCCATGTATCAAAGACAAAGAAATCAAAGCTGGGGTTGTAAGAGGGAGCTGACGCTGTGGGGGTTTCAGATCTGGATGGAGGCTTGGCCGCCTGGACTCCTACAACCATGAGTGACAGAAGAACCATATGAGTCTGGGGAGCAAGAAACAAACCCCCCGGATATATTCCAGGGTCTCCAAAG-C
• rs1554998040
• NM_145200.5:c.800-18_*795del

Variant summary

Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PVS1_Strong PM2 PP5

The ENST00000438189.6(CABP4):​c.485-18_*795del variant causes a exon loss, splice acceptor, 3 prime UTR truncation, 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 Likely pathogenic (no stars).

• Frequency: Genomes: not found (cov: 32)
• Consequence: CABP4 ENST00000438189.6 exon_loss, splice_acceptor, 3_prime_UTR_truncation, splice_region, intron
• Clinical Significance: Likely pathogenic no assertion criteria provided P:1
• 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]

ACMG classification

Verdict is Likely_pathogenic. Variant got 7 ACMG points.

• PVS1: Splicing +-2 bp (donor or acceptor) variant, product NOT destroyed by NMD, known LOF gene, truncates 1.0077972709551657 fraction of the gene. 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 rank	MANE	Protein	UniProt
CABP4	NM_145200.5	c.800-18_*795del	p.Glu267fs	frameshift_variant, stop_lost, splice_region_variant	Exon 6 of 6	ENST00000325656.7	NP_660201.1
CABP4	NM_145200.5	c.800-18_*795del		splice_acceptor_variant, splice_region_variant, 3_prime_UTR_variant, intron_variant	Exon 6 of 6	ENST00000325656.7	NP_660201.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CABP4	ENST00000325656.7	c.800-18_*795del	p.Glu267fs	frameshift_variant, stop_lost, splice_region_variant	Exon 6 of 6	1	NM_145200.5	ENSP00000324960.5
CABP4	ENST00000325656.7	c.800-18_*795del		splice_acceptor_variant, splice_region_variant, 3_prime_UTR_variant, intron_variant	Exon 6 of 6	1	NM_145200.5	ENSP00000324960.5
CABP4	ENST00000438189.6	c.485-18_*795del		exon_loss_variant, splice_acceptor_variant, 3_prime_UTR_truncation, splice_region_variant, intron_variant	Exon 7 of 7	1		ENSP00000401555.2
CABP4	ENST00000438189.6	c.485-18_*795del		downstream_gene_variant		1		ENSP00000401555.2

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: Likely pathogenic

Submissions summary: Pathogenic:1

Revision: no assertion criteria provided

Submissions by phenotype

Retinal dystrophy Pathogenic:1

-

NIHR Bioresource Rare Diseases, University of Cambridge

Significance: Likely pathogenic

Review Status: no assertion criteria provided

Collection Method: research

- -

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: rs1554998040; hg19: chr11-67226083;