rs878853152

Variant names:

• chrX-120547153-CTG-C
• rs878853152
• NM_001079872.2:c.757_758delCA

Variant summary

Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1 PM2 PP5_Moderate

The NM_001079872.2(CUL4B):​c.757_758delCA​(p.Gln253AspfsTer11) variant causes a frameshift change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (★). Variant results in nonsense mediated mRNA decay.

• Frequency: Genomes: not found (cov: 23)
• Consequence: CUL4B NM_001079872.2 frameshift
• Clinical Significance: Pathogenic criteria provided, single submitter P:1
• Conservation: PhyloP100: 10.0

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]

ACMG classification

Verdict is Pathogenic. Variant got 12 ACMG points.

• PVS1: Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant X-120547153-CTG-C is Pathogenic according to our data. Variant chrX-120547153-CTG-C is described in ClinVar as [Pathogenic]. Clinvar id is 235856.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-120547153-CTG-C is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CUL4B	NM_001079872.2	c.757_758delCA	p.Gln253AspfsTer11	frameshift_variant	Exon 3 of 20	ENST00000371322.11	NP_001073341.1
CUL4B	NM_003588.4	c.811_812delCA	p.Gln271AspfsTer11	frameshift_variant	Exon 5 of 22		NP_003579.3
CUL4B	NM_001330624.2	c.772_773delCA	p.Gln258AspfsTer11	frameshift_variant	Exon 4 of 21		NP_001317553.1
CUL4B	NM_001369145.1	c.223_224delCA	p.Gln75AspfsTer11	frameshift_variant	Exon 3 of 20		NP_001356074.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CUL4B	ENST00000371322.11	c.757_758delCA	p.Gln253AspfsTer11	frameshift_variant	Exon 3 of 20	1	NM_001079872.2	ENSP00000360373.5
CUL4B	ENST00000681206.1	c.871_872delCA	p.Gln291AspfsTer11	frameshift_variant	Exon 6 of 23			ENSP00000505480.1
CUL4B	ENST00000680673.1	c.811_812delCA	p.Gln271AspfsTer11	frameshift_variant	Exon 5 of 22			ENSP00000505084.1
CUL4B	ENST00000681253.1	c.811_812delCA	p.Gln271AspfsTer11	frameshift_variant	Exon 6 of 23			ENSP00000506259.1
CUL4B	ENST00000681652.1	c.811_812delCA	p.Gln271AspfsTer11	frameshift_variant	Exon 8 of 25			ENSP00000505176.1
CUL4B	ENST00000336592.11	c.772_773delCA	p.Gln258AspfsTer11	frameshift_variant	Exon 4 of 21	5		ENSP00000338919.6
CUL4B	ENST00000674137.11	c.757_758delCA	p.Gln253AspfsTer11	frameshift_variant	Exon 3 of 20			ENSP00000501019.6
CUL4B	ENST00000681090.1	c.757_758delCA	p.Gln253AspfsTer11	frameshift_variant	Exon 3 of 20			ENSP00000506288.1
CUL4B	ENST00000404115.8	c.757_758delCA	p.Gln253AspfsTer11	frameshift_variant	Exon 3 of 19	1		ENSP00000384109.4
CUL4B	ENST00000679927.1	c.412_413delCA	p.Gln138AspfsTer11	frameshift_variant	Exon 4 of 21			ENSP00000505603.1
CUL4B	ENST00000371323.3	c.223_224delCA	p.Gln75AspfsTer11	frameshift_variant	Exon 3 of 20	5		ENSP00000360374.3
CUL4B	ENST00000680474.1	c.199_200delCA	p.Gln67fs	frameshift_variant	Exon 2 of 20			ENSP00000505562.1
CUL4B	ENST00000679844.1	c.199_200delCA	p.Gln67fs	frameshift_variant	Exon 2 of 18			ENSP00000505239.1
CUL4B	ENST00000673919.1	n.*204_*205delCA		non_coding_transcript_exon_variant	Exon 4 of 21			ENSP00000500994.1
CUL4B	ENST00000674073.2	n.199_200delCA		non_coding_transcript_exon_variant	Exon 2 of 18			ENSP00000501262.2
CUL4B	ENST00000679405.1	n.341_342delCA		non_coding_transcript_exon_variant	Exon 5 of 22			ENSP00000504985.1
CUL4B	ENST00000679432.1	n.860_861delCA		non_coding_transcript_exon_variant	Exon 5 of 22			ENSP00000505343.1
CUL4B	ENST00000680918.1	n.199_200delCA		non_coding_transcript_exon_variant	Exon 2 of 18			ENSP00000505955.1
CUL4B	ENST00000681080.1	n.245_246delCA		non_coding_transcript_exon_variant	Exon 3 of 20			ENSP00000505898.1
CUL4B	ENST00000681189.1	n.199_200delCA		non_coding_transcript_exon_variant	Exon 2 of 20			ENSP00000505973.1
CUL4B	ENST00000681333.1	n.757_758delCA		non_coding_transcript_exon_variant	Exon 3 of 17			ENSP00000505739.1
CUL4B	ENST00000681869.1	n.199_200delCA		non_coding_transcript_exon_variant	Exon 2 of 17			ENSP00000505597.1
CUL4B	ENST00000681908.1	n.199_200delCA		non_coding_transcript_exon_variant	Exon 2 of 20			ENSP00000505777.1
CUL4B	ENST00000673919.1	n.*204_*205delCA		3_prime_UTR_variant	Exon 4 of 21			ENSP00000500994.1

Frequencies

GnomAD3 genomes Cov.: 23

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

GnomAD4 genome Cov.: 23

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: criteria provided, single submitter

Submissions by phenotype

Intellectual disability Pathogenic:1

Jul 25, 2014

Diagnostic Laboratory, Strasbourg University Hospital

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs878853152; hg19: chrX-119681008;