NM_006493.4:c.566-42_*46del

Variant names:

• 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. PM4 PP5

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: Genomes: not found (cov: 32)
• Consequence: CLN5 NM_006493.4 stop_lost, conservative_inframe_deletion, splice_region
• Clinical Significance: Pathogenic no assertion criteria provided P:1
• Conservation: PhyloP100: 2.33
• Publications: 0 publications found

Genes affected

CLN5 (HGNC:2076): (CLN5 intracellular trafficking protein) This gene is one of eight which have been associated with neuronal ceroid lipofuscinoses (NCL). Also referred to as Batten disease, NCL comprises a class of autosomal recessive, neurodegenerative disorders affecting children. The genes responsible likely encode proteins involved in the degradation of post-translationally modified proteins in lysosomes. The primary defect in NCL disorders is thought to be associated with lysosomal storage function.[provided by RefSeq, Oct 2008]

ENSG00000283208 (HGNC:):

FBXL3 (HGNC:13599): (F-box and leucine rich repeat protein 3) This gene encodes a member of the F-box protein family which is characterized by an approximately 40 amino acid motif, the F-box. The F-box proteins constitute one of the four subunits of ubiquitin protein ligase complex called SCFs (SKP1-cullin-F-box), which function in phosphorylation-dependent ubiquitination. The F-box proteins are divided into 3 classes: Fbws containing WD-40 domains, Fbls containing leucine-rich repeats, and Fbxs containing either different protein-protein interaction modules or no recognizable motifs. The protein encoded by this gene belongs to the Fbls class and, in addition to an F-box, contains several tandem leucine-rich repeats and is localized in the nucleus. [provided by RefSeq, Jul 2008]

FBXL3 Gene-Disease associations (from GenCC):

• intellectual disability, short stature, facial anomalies, and joint dislocations

  Inheritance: AR Classification: LIMITED Submitted by: Ambry Genetics

ACMG classification

Our verdict: Uncertain_significance. The variant received 3 ACMG points.

• PM4: Stoplost variant in NM_006493.4
• PP5: Variant 13-77000415-AGCTTTGTTCACTAGGTGACTTTGTTTTGTTTTTTTAAACTAGGAAACATGTTCAACCAAATGGCAAAGTGGGTGAAACAGGACAATGAAACAGGAATTTATTATGAGACATGGAATGTAAAAGCCAGCCCAGAAAAGGGGGCAGAGACATGGTTTGATTCCTACGACTGTTCCAAATTTGTGTTAAGGACCTTTAACAAGTTGGCTGAATTTGGAGCAGAGTTCAAGAACATAGAAACCAACTATACAAGAATATTTCTTTACAGTGGAGAACCTACTTATCTGGGAAATGAAACATCTGTTTTTGGGCCAACAGGAAACAAGACTCTTGGTTTAGCCATAAAAAGATTTTATTACCCCTTCAAACCACATTTGCCAACTAAAGAATTTCTGTTGAGTCTCTTGCAAATTTTTGATGCAGTGATTGTGCACAAACAGTTCTATTTGTTTTATAATTTTGAATATTGGTTTTTACCTATGAAATTCCCTTTTATTAAAATAACATATGAAGAAATCCCTTTACCTATCAGAAACAAAACACTCTCTGGTTTATAAAACACCTTAATTCTACTGCTCTTTTTTCTCCAATCACCAGCATCTG-A is Pathogenic according to our data. Variant chr13-77000415-AGCTTTGTTCACTAGGTGACTTTGTTTTGTTTTTTTAAACTAGGAAACATGTTCAACCAAATGGCAAAGTGGGTGAAACAGGACAATGAAACAGGAATTTATTATGAGACATGGAATGTAAAAGCCAGCCCAGAAAAGGGGGCAGAGACATGGTTTGATTCCTACGACTGTTCCAAATTTGTGTTAAGGACCTTTAACAAGTTGGCTGAATTTGGAGCAGAGTTCAAGAACATAGAAACCAACTATACAAGAATATTTCTTTACAGTGGAGAACCTACTTATCTGGGAAATGAAACATCTGTTTTTGGGCCAACAGGAAACAAGACTCTTGGTTTAGCCATAAAAAGATTTTATTACCCCTTCAAACCACATTTGCCAACTAAAGAATTTCTGTTGAGTCTCTTGCAAATTTTTGATGCAGTGATTGTGCACAAACAGTTCTATTTGTTTTATAATTTTGAATATTGGTTTTTACCTATGAAATTCCCTTTTATTAAAATAACATATGAAGAAATCCCTTTACCTATCAGAAACAAAACACTCTCTGGTTTATAAAACACCTTAATTCTACTGCTCTTTTTTCTCCAATCACCAGCATCTG-A is described in ClinVar as [Pathogenic]. Clinvar id is 2571.Status of the report is no_assertion_criteria_provided, 0 stars.

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

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

Neuronal ceroid lipofuscinosis 5 Pathogenic:1

Feb 16, 2010

OMIM

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		2.3

Splicing

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

Other links and lift over

dbSNP: rs1555274312; hg19: chr13-77574550;