X-120527062-CTTTT-CTTTTTTT

Variant names:

• chrX-120527062-C-CTTT
• rs918835696
• NM_001079872.2:c.2593-209_2593-207dupAAA

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_001079872.2(CUL4B):​c.2593-209_2593-207dupAAA variant causes a 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: 𝑓 0.0 (0 hom., 0 hem., cov: 21)
  • Failed GnomAD Quality Control
• Consequence: CUL4B NM_001079872.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.17
• Publications: 0 publications found

Genes affected

CUL4B (HGNC:2555): (cullin 4B) This gene is a member of the cullin family. The encoded protein forms a complex that functions as an E3 ubiquitin ligase and catalyzes the polyubiquitination of specific protein substrates in the cell. The protein interacts with a ring finger protein, and is required for the proteolysis of several regulators of DNA replication including chromatin licensing and DNA replication factor 1 and cyclin E. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

CUL4B Gene-Disease associations (from GenCC):

• X-linked intellectual disability, Cabezas type

  Inheritance: XL Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: ClinGen, G2P, Labcorp Genetics (formerly Invitae), Orphanet

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001079872.2. 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
	CUL4B	NM_001079872.2	MANE Select	c.2593-209_2593-207dupAAA		intron	N/A	NP_001073341.1	Q13620-1
	CUL4B	NM_003588.4		c.2647-209_2647-207dupAAA		intron	N/A	NP_003579.3
	CUL4B	NM_001330624.2		c.2608-209_2608-207dupAAA		intron	N/A	NP_001317553.1	K4DI93

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CUL4B	ENST00000371322.11	TSL:1 MANE Select	c.2593-207_2593-206insAAA		intron	N/A	ENSP00000360373.5	Q13620-1
	CUL4B	ENST00000681206.1		c.2707-207_2707-206insAAA		intron	N/A	ENSP00000505480.1	A0A7P0T954
	CUL4B	ENST00000680673.1		c.2647-207_2647-206insAAA		intron	N/A	ENSP00000505084.1	Q13620-2

Frequencies

GnomAD3 genomes AF: 0.00 AC: 0 AN: 100845 Hom.: 0 Cov.: 21

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

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

GnomAD4 genome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 100845 Hom.: 0 Cov.: 21 AF XY: 0.00 AC XY: 0 AN XY: 27711

African (AFR) AF: 0.00 AC: 0 AN: 28125

American (AMR) AF: 0.00 AC: 0 AN: 9335

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2443

East Asian (EAS) AF: 0.00 AC: 0 AN: 3304

South Asian (SAS) AF: 0.00 AC: 0 AN: 2354

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 4101

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 212

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 49021

Other (OTH) AF: 0.00 AC: 0 AN: 1318

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs918835696; hg19: chrX-119660917;