rs267608431

Positions:

• chrX-18564525-AGA-AATATATATATATATATATATAT
• chrX-18564525-AGA-AATATATATATATATATATATATAT
• chrX-18564525-AGA-AATATATATATATATATATATATATAT

Variant summary

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

The NM_001323289.2(CDKL5):​c.145+4_145+5delinsATATATATATATATATATATAT variant causes a splice donor 5th base, intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 19)
• Consequence: CDKL5 NM_001323289.2 splice_donor_5th_base, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.26

Genes affected

CDKL5 (HGNC:11411): (cyclin dependent kinase like 5) This gene is a member of Ser/Thr protein kinase family and encodes a phosphorylated protein with protein kinase activity. Mutations in this gene have been associated with X-linked infantile spasm syndrome (ISSX), also known as X-linked West syndrome, and Rett syndrome (RTT). Alternate transcriptional splice variants have been characterized. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CDKL5	NM_001323289.2	c.145+4_145+5delinsATATATATATATATATATATAT		splice_donor_5th_base_variant, intron_variant		ENST00000623535.2	NP_001310218.1
CDKL5	NM_001037343.2	c.145+4_145+5delinsATATATATATATATATATATAT		splice_donor_5th_base_variant, intron_variant			NP_001032420.1
CDKL5	NM_003159.3	c.145+4_145+5delinsATATATATATATATATATATAT		splice_donor_5th_base_variant, intron_variant			NP_003150.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CDKL5	ENST00000623535.2	c.145+4_145+5delinsATATATATATATATATATATAT		splice_donor_5th_base_variant, intron_variant		1	NM_001323289.2	ENSP00000485244	P1

Frequencies

GnomAD3 genomes Cov.: 19

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

GnomAD4 genome Cov.: 19

ClinVar

Not reported in ClinVar

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: rs267608431; hg19: chrX-18582646;