rs1553442237

Variant names:

• chr2-112756885-ACATTTACCATTTCCTTGATCTGTTAACTGCTGCTTTGTAGTTTTCAATTGCTCTATATTAAGTGACCCCACAGGTTTTCTTGACAGTTCTCCTGTTGTGGACGATCCAGCTTCACACTGTTGAAAACTCTTGCTAGAAGGCTTAGAGTATGGGTTAGAAGAAACACATTCTGAAGTCAGCCTTTTGCCCAGAAGTTTTGGTGGCTCCAACTTCGGCTTCTGGGACCCTGCAGTATTAGGTGGTCTGGGCTGGAGTTTAATGCTGATGGACCTTTTAGGTTTGACAGGCAAAACAACATGGTTGGTAACATCATTTTTGGGTCTAATAGT-A
• rs1553442237
• NM_152515.5:c.157_485del

Variant summary

Our verdict is Likely pathogenic. The variant received 9 ACMG points: 9P and 0B. PVS1 PP5

The NM_152515.5(CKAP2L):​c.157_485del​(p.Thr53TyrfsTer6) variant causes a frameshift, 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). Variant results in nonsense mediated mRNA decay.

• Frequency: Genomes: not found (cov: 32)
• Consequence: CKAP2L NM_152515.5 frameshift, splice_region
• Clinical Significance: Pathogenic no assertion criteria provided P:1
• Conservation: PhyloP100: 1.92
• Publications: 0 publications found

Genes affected

CKAP2L (HGNC:26877): (cytoskeleton associated protein 2 like) The protein encoded by this gene is thought to be a mitotic spindle protein important to neural stem or progenitor cells. Mutations in this gene have been associated with spindle organization defects, including mitotic spindle defects, lagging chromosomes, and chromatin bridges. There is evidence that mutations in this gene are associated with Filippi syndrome, characterized by growth defects, microcephaly, intellectual disability, facial feature defects, and syndactyly. There is a pseudogene of this gene on chromosome 20. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2015]

CKAP2L Gene-Disease associations (from GenCC):

• Filippi syndrome

  Inheritance: AR, AD Classification: DEFINITIVE, STRONG, MODERATE, SUPPORTIVE Submitted by: Orphanet, Labcorp Genetics (formerly Invitae), Ambry Genetics, G2P

ACMG classification

Our verdict: Likely_pathogenic. The variant received 9 ACMG points.

• PVS1: Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
• PP5: Variant 2-112756885-ACATTTACCATTTCCTTGATCTGTTAACTGCTGCTTTGTAGTTTTCAATTGCTCTATATTAAGTGACCCCACAGGTTTTCTTGACAGTTCTCCTGTTGTGGACGATCCAGCTTCACACTGTTGAAAACTCTTGCTAGAAGGCTTAGAGTATGGGTTAGAAGAAACACATTCTGAAGTCAGCCTTTTGCCCAGAAGTTTTGGTGGCTCCAACTTCGGCTTCTGGGACCCTGCAGTATTAGGTGGTCTGGGCTGGAGTTTAATGCTGATGGACCTTTTAGGTTTGACAGGCAAAACAACATGGTTGGTAACATCATTTTTGGGTCTAATAGT-A is Pathogenic according to our data. Variant chr2-112756885-ACATTTACCATTTCCTTGATCTGTTAACTGCTGCTTTGTAGTTTTCAATTGCTCTATATTAAGTGACCCCACAGGTTTTCTTGACAGTTCTCCTGTTGTGGACGATCCAGCTTCACACTGTTGAAAACTCTTGCTAGAAGGCTTAGAGTATGGGTTAGAAGAAACACATTCTGAAGTCAGCCTTTTGCCCAGAAGTTTTGGTGGCTCCAACTTCGGCTTCTGGGACCCTGCAGTATTAGGTGGTCTGGGCTGGAGTTTAATGCTGATGGACCTTTTAGGTTTGACAGGCAAAACAACATGGTTGGTAACATCATTTTTGGGTCTAATAGT-A is described in ClinVar as Pathogenic. ClinVar VariationId is 162388.Status of the report is no_assertion_criteria_provided, 0 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CKAP2L	NM_152515.5	c.157_485del	p.Thr53TyrfsTer6	frameshift_variant, splice_region_variant	Exon 4 of 9	ENST00000302450.11	NP_689728.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CKAP2L	ENST00000302450.11	c.157_485del	p.Thr53TyrfsTer6	frameshift_variant, splice_region_variant	Exon 4 of 9	1	NM_152515.5	ENSP00000305204.6

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

Filippi syndrome Pathogenic:1

Nov 06, 2014

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		1.9
Mutation Taster		=15/185	disease causing (ClinVar)

Splicing

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

Other links and lift over

dbSNP: rs1553442237; hg19: chr2-113514462;