NM_001323289.2:c.-163+16465A>G

Variant names:

• chrX-18442160-A-G
• rs2283722
• NM_001323289.2:c.-163+16465A>G

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_001323289.2(CDKL5):​c.-163+16465A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0269 in 110,730 control chromosomes in the GnomAD database, including 89 homozygotes. There are 922 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.027 (88 hom., 922 hem., cov: 22)
  • Exomes 𝑓: 0.034 (1 hom. 0 hem.)
• Consequence: CDKL5 NM_001323289.2 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -1.33
• Publications: 0 publications found

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]

CDKL5 Gene-Disease associations (from GenCC):

• CDKL5 disorder

  Inheritance: XL Classification: DEFINITIVE Submitted by: ClinGen
• developmental and epileptic encephalopathy, 2

  Inheritance: XL Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, G2P, Labcorp Genetics (formerly Invitae), Ambry Genetics
• atypical Rett syndrome

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• genetic developmental and epileptic encephalopathy

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• infantile spasms

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• precocious puberty

  Inheritance: XL Classification: LIMITED Submitted by: Ambry Genetics

ACMG classification

Our verdict: Benign. The variant received -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BP6: Variant X-18442160-A-G is Benign according to our data. Variant chrX-18442160-A-G is described in ClinVar as Benign. ClinVar VariationId is 1222003.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.177 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001323289.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDKL5	NM_001323289.2	MANE Select	c.-163+16465A>G		intron	N/A	NP_001310218.1	O76039-2
	CDKL5	NM_003159.3		c.-163+16465A>G		intron	N/A	NP_003150.1	O76039-1
	CDKL5	NM_001037343.2		c.-313A>G		upstream_gene	N/A	NP_001032420.1	O76039-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDKL5	ENST00000623535.2	TSL:1 MANE Select	c.-163+16465A>G		intron	N/A	ENSP00000485244.1	O76039-2
	CDKL5	ENST00000379996.7	TSL:1	c.-163+16465A>G		intron	N/A	ENSP00000369332.3	O76039-1
	CDKL5	ENST00000674046.1		c.-163+16465A>G		intron	N/A	ENSP00000501174.1	A0A669KBC2

Frequencies

GnomAD3 genomes AF: 0.0267 AC: 2956 AN: 110619 Hom.: 88 Cov.: 22

Gnomad AFR AF: 0.0611

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0210

Gnomad ASJ AF: 0.000379

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.0641

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00424

Gnomad NFE AF: 0.000435

Gnomad OTH AF: 0.0295

GnomAD4 exome AF: 0.0339 AC: 2 AN: 59 Hom.: 1 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 27

African (AFR) AF: 0.667 AC: 2 AN: 3

American (AMR) AF: 0.00 AC: 0 AN: 2

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 0.00 AC: 0 AN: 2

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 1

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 50

Other (OTH) AF: 0.00 AC: 0 AN: 1

GnomAD4 genome AF: 0.0269 AC: 2972 AN: 110671 Hom.: 88 Cov.: 22 AF XY: 0.0280 AC XY: 922 AN XY: 32983

African (AFR) AF: 0.0614 AC: 1869 AN: 30419

American (AMR) AF: 0.0210 AC: 217 AN: 10351

Ashkenazi Jewish (ASJ) AF: 0.000379 AC: 1 AN: 2639

East Asian (EAS) AF: 0.189 AC: 650 AN: 3441

South Asian (SAS) AF: 0.0636 AC: 165 AN: 2596

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 5948

Middle Eastern (MID) AF: 0.00465 AC: 1 AN: 215

European-Non Finnish (NFE) AF: 0.000435 AC: 23 AN: 52871

Other (OTH) AF: 0.0304 AC: 46 AN: 1512

Alfa AF: 0.0266 Hom.: 65

Bravo AF: 0.0329

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	not provided (2)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.41
DANN	Benign	0.62
PhyloP100		-1.3
PromoterAI		0.013	Neutral
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs2283722; hg19: chrX-18460280;