9-707445-TGCAGCTTCTCTCCTGTTAATGGAGTTTCAGACAGTCCTGGAGACAGGTCTGGCTGCTGCAGCTTCTCTCCTGTTAATGGAGTTTCAGACAGTCCTGGAGACAGGTCTGGCTGCTGCAGCTTCTCTCCTGTTAATGGAGTTTCAGACATTCCTGGAGACAGGTCTGGCTGCTGCAGCTTCTCTCCTGTTAATGGAGTTTCAGACAGTCCTGGAGACAGGTCTGGCTGCTGCAGCTTCTCTCCTGTTAATGGAGTTTCAGACAGTCCTGGAGACAGGTCTGGCTGCTGCAGCTTCTCTCCTGTTAATGGAGTTTCAGACATTCCTGGAGACAGGTCTGGCTGCTGCAGCTTCTCTCCTGTTAATGGAGTTTCAGACAGTCCTGGAGACAGGTCTGGCTGCTGCAGCTTCTCTCCTGTTAATGGAGTTTCAGACAGTCCTGGAGACAGGTCTGGCTGCTGCAGCTTCTCTCCTGTTAATGGAGTTTCAGACAGTCCTGGAGACAGGTCTGGCTGCTGCAGCTTCTCTCCTGTTAATGGAGTTTCAGACATTCCTGGAGACAGGTCTGGCTGCTGC-T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The XM_017015393.3(LOC107987042):c.309_880del(p.Gln104AlafsTer32) variant causes a frameshift 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 Uncertain significance (no stars).

• Frequency: Genomes: not found (cov: 31)
• Consequence: LOC107987042 XM_017015393.3 frameshift
• Clinical Significance: Uncertain significance no assertion criteria provided U:1
• Conservation: PhyloP100: 1.24

Genes affected

LOC107987042 (HGNC:):

KANK1 (HGNC:19309): (KN motif and ankyrin repeat domains 1) The protein encoded by this gene belongs to the Kank family of proteins, which contain multiple ankyrin repeat domains. This family member functions in cytoskeleton formation by regulating actin polymerization. This gene is a candidate tumor suppressor for renal cell carcinoma. Mutations in this gene cause cerebral palsy spastic quadriplegic type 2, a central nervous system development disorder. A t(5;9) translocation results in fusion of the platelet-derived growth factor receptor beta gene (PDGFRB) on chromosome 5 with this gene in a myeloproliferative neoplasm featuring severe thrombocythemia. Alternative splicing of this gene results in multiple transcript variants. A related pseudogene has been identified on chromosome 20. [provided by RefSeq, Dec 2014]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107987042	XM_017015393.3	c.309_880del	p.Gln104AlafsTer32	frameshift_variant	1/1
KANK1	NM_015158.5	c.38-3358_38-2787del		intron_variant		ENST00000382297.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KANK1	ENST00000382297.7	c.38-3358_38-2787del		intron_variant		1	NM_015158.5	P2

Frequencies

GnomAD3 genomes Cov.: 31

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 31

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: no assertion criteria provided

Submissions by phenotype

Schizophrenia Uncertain:1

Uncertain significance, no assertion criteria provided

case-control

Department of Psychiatry, The University of Hong Kong

Nov 11, 2022

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Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr9-707445;