rs672601323

Positions:

• chrX-18608911-AG-NNNNNNNNNNNNNNNNNN

Variant summary

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

The NM_001323289.2(CDKL5):​c.2045_2046delAGinsNNNNNNNNNNNNNNNNNN​(p.Glu682delins?????????????????????) variant causes a missense, splice region change. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 N/A (N/A hom., N/A hem., cov:)
  • Exomes 𝑓: N/A (N/A hom. N/A hem.)
• Consequence: CDKL5 NM_001323289.2 missense, splice_region
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned

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.2045_2046delAGinsNNNNNNNNNNNNNNNNNN	p.Glu682delins?????????????????????	missense_variant, splice_region_variant		ENST00000623535.2	NP_001310218.1
CDKL5	NM_001037343.2	c.2045_2046delAGinsNNNNNNNNNNNNNNNNNN	p.Glu682delins?????????????????????	missense_variant, splice_region_variant			NP_001032420.1
CDKL5	NM_003159.3	c.2045_2046delAGinsNNNNNNNNNNNNNNNNNN	p.Glu682delins?????????????????????	missense_variant, splice_region_variant			NP_003150.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CDKL5	ENST00000623535.2	c.2045_2046delAGinsNNNNNNNNNNNNNNNNNN	p.Glu682delins?????????????????????	missense_variant, splice_region_variant		1	NM_001323289.2	ENSP00000485244.1

Frequencies

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

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

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

No publications associated with this variant yet.

Other links and lift over

hg19: chrX-18627031;