NM_006493.4:c.566-42_*46del
- chr13-77000415-AGCTTTGTTCACTAGGTGACTTTGTTTTGTTTTTTTAAACTAGGAAACATGTTCAACCAAATGGCAAAGTGGGTGAAACAGGACAATGAAACAGGAATTTATTATGAGACATGGAATGTAAAAGCCAGCCCAGAAAAGGGGGCAGAGACATGGTTTGATTCCTACGACTGTTCCAAATTTGTGTTAAGGACCTTTAACAAGTTGGCTGAATTTGGAGCAGAGTTCAAGAACATAGAAACCAACTATACAAGAATATTTCTTTACAGTGGAGAACCTACTTATCTGGGAAATGAAACATCTGTTTTTGGGCCAACAGGAAACAAGACTCTTGGTTTAGCCATAAAAAGATTTTATTACCCCTTCAAACCACATTTGCCAACTAAAGAATTTCTGTTGAGTCTCTTGCAAATTTTTGATGCAGTGATTGTGCACAAACAGTTCTATTTGTTTTATAATTTTGAATATTGGTTTTTACCTATGAAATTCCCTTTTATTAAAATAACATATGAAGAAATCCCTTTACCTATCAGAAACAAAACACTCTCTGGTTTATAAAACACCTTAATTCTACTGCTCTTTTTTCTCCAATCACCAGCATCTG-A
- rs1555274312
- NM_006493.4:c.566-42_*46del
Variant summary
Our verdict is Uncertain significance. The variant received 3 ACMG points: 3P and 0B. PM4PP5
The NM_006493.4(CLN5):c.566-42_*46del(p.Gly189_Ter359delins???) variant causes a stop lost, conservative inframe deletion, splice region change involving the alteration of a non-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).
Frequency
Consequence
NM_006493.4 stop_lost, conservative_inframe_deletion, splice_region
Scores
Clinical Significance
Conservation
Publications
- intellectual disability, short stature, facial anomalies, and joint dislocationsInheritance: AR Classification: LIMITED Submitted by: Ambry Genetics
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ACMG classification
Our verdict: Uncertain_significance. The variant received 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CLN5 | NM_006493.4 | c.566-42_*46del | p.Gly189_Ter359delins??? | stop_lost, conservative_inframe_deletion, splice_region_variant | Exon 4 of 4 | ENST00000377453.9 | NP_006484.2 | |
CLN5 | NM_006493.4 | c.566-42_*46del | splice_acceptor_variant, splice_region_variant, 3_prime_UTR_variant, intron_variant | Exon 4 of 4 | ENST00000377453.9 | NP_006484.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CLN5 | ENST00000377453.9 | c.566-42_*46del | p.Gly189_Ter359delins??? | stop_lost, conservative_inframe_deletion, splice_region_variant | Exon 4 of 4 | 1 | NM_006493.4 | ENSP00000366673.5 | ||
CLN5 | ENST00000377453.9 | c.566-42_*46del | splice_acceptor_variant, splice_region_variant, 3_prime_UTR_variant, intron_variant | Exon 4 of 4 | 1 | NM_006493.4 | ENSP00000366673.5 | |||
ENSG00000283208 | ENST00000638147.2 | c.565+4289_565+4888del | intron_variant | Intron 3 of 4 | 5 | ENSP00000490953.2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Neuronal ceroid lipofuscinosis 5 Pathogenic:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at