X-120530154-CTAAG-C

Variant names:

• chrX-120530154-CTAAG-C
• rs1602567594
• NM_001079872.2:c.2536_2539delCTTA

Variant summary

Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PVS1_Moderate PM2 PP5_Moderate

The NM_001079872.2(CUL4B):​c.2536_2539delCTTA​(p.Leu846AlafsTer13) 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 (★).

• Frequency: Genomes: not found (cov: 23)
• Consequence: CUL4B NM_001079872.2 frameshift
• Clinical Significance: Pathogenic criteria provided, single submitter P:1 O:1
• Conservation: PhyloP100: 8.95

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 Likely_pathogenic. Variant got 6 ACMG points.

• PVS1: Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant is located in the 3'-most 50 bp of the penultimate exon, not predicted to undergo nonsense mediated mRNA decay. Fraction of 0.0565 CDS is truncated, and there are 0 pathogenic variants in the truncated region.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant X-120530154-CTAAG-C is Pathogenic according to our data. Variant chrX-120530154-CTAAG-C is described in ClinVar as [Pathogenic]. Clinvar id is 817034.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-120530154-CTAAG-C is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CUL4B	NM_001079872.2	c.2536_2539delCTTA	p.Leu846AlafsTer13	frameshift_variant	Exon 19 of 20	ENST00000371322.11	NP_001073341.1
CUL4B	NM_003588.4	c.2590_2593delCTTA	p.Leu864AlafsTer13	frameshift_variant	Exon 21 of 22		NP_003579.3
CUL4B	NM_001330624.2	c.2551_2554delCTTA	p.Leu851AlafsTer13	frameshift_variant	Exon 20 of 21		NP_001317553.1
CUL4B	NM_001369145.1	c.2002_2005delCTTA	p.Leu668AlafsTer13	frameshift_variant	Exon 19 of 20		NP_001356074.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CUL4B	ENST00000371322.11	c.2536_2539delCTTA	p.Leu846AlafsTer13	frameshift_variant	Exon 19 of 20	1	NM_001079872.2	ENSP00000360373.5
CUL4B	ENST00000681206.1	c.2650_2653delCTTA	p.Leu884AlafsTer13	frameshift_variant	Exon 22 of 23			ENSP00000505480.1
CUL4B	ENST00000680673.1	c.2590_2593delCTTA	p.Leu864AlafsTer13	frameshift_variant	Exon 21 of 22			ENSP00000505084.1
CUL4B	ENST00000681253.1	c.2590_2593delCTTA	p.Leu864AlafsTer13	frameshift_variant	Exon 22 of 23			ENSP00000506259.1
CUL4B	ENST00000681652.1	c.2590_2593delCTTA	p.Leu864AlafsTer13	frameshift_variant	Exon 24 of 25			ENSP00000505176.1
CUL4B	ENST00000336592.11	c.2551_2554delCTTA	p.Leu851AlafsTer13	frameshift_variant	Exon 20 of 21	5		ENSP00000338919.6
CUL4B	ENST00000674137.11	c.2542_2545delCTTA	p.Leu848AlafsTer13	frameshift_variant	Exon 19 of 20			ENSP00000501019.6
CUL4B	ENST00000681090.1	c.2443_2446delCTTA	p.Leu815AlafsTer13	frameshift_variant	Exon 19 of 20			ENSP00000506288.1
CUL4B	ENST00000679927.1	c.2191_2194delCTTA	p.Leu731AlafsTer13	frameshift_variant	Exon 20 of 21			ENSP00000505603.1
CUL4B	ENST00000371323.3	c.2002_2005delCTTA	p.Leu668AlafsTer13	frameshift_variant	Exon 19 of 20	5		ENSP00000360374.3
CUL4B	ENST00000680474.1	c.1978_1981delCTTA	p.Leu660fs	frameshift_variant	Exon 18 of 20			ENSP00000505562.1
CUL4B	ENST00000679844.1	c.1873_1876delCTTA	p.Leu625fs	frameshift_variant	Exon 17 of 18			ENSP00000505239.1
CUL4B	ENST00000404115.8	c.2439+2264_2439+2267delCTTA		intron_variant	Intron 18 of 18	1		ENSP00000384109.4
CUL4B	ENST00000673919.1	n.*1983_*1986delCTTA		non_coding_transcript_exon_variant	Exon 20 of 21			ENSP00000500994.1
CUL4B	ENST00000674073.2	n.*92_*95delCTTA		non_coding_transcript_exon_variant	Exon 17 of 18			ENSP00000501262.2
CUL4B	ENST00000679405.1	n.*1745_*1748delCTTA		non_coding_transcript_exon_variant	Exon 21 of 22			ENSP00000504985.1
CUL4B	ENST00000679432.1	n.*1745_*1748delCTTA		non_coding_transcript_exon_variant	Exon 21 of 22			ENSP00000505343.1
CUL4B	ENST00000680918.1	n.*1452_*1455delCTTA		non_coding_transcript_exon_variant	Exon 17 of 18			ENSP00000505955.1
CUL4B	ENST00000681080.1	n.*1745_*1748delCTTA		non_coding_transcript_exon_variant	Exon 19 of 20			ENSP00000505898.1
CUL4B	ENST00000681189.1	n.*702_*705delCTTA		non_coding_transcript_exon_variant	Exon 19 of 20			ENSP00000505973.1
CUL4B	ENST00000681333.1	n.*3429_*3432delCTTA		non_coding_transcript_exon_variant	Exon 16 of 17			ENSP00000505739.1
CUL4B	ENST00000681908.1	n.*708_*711delCTTA		non_coding_transcript_exon_variant	Exon 19 of 20			ENSP00000505777.1
CUL4B	ENST00000673919.1	n.*1983_*1986delCTTA		3_prime_UTR_variant	Exon 20 of 21			ENSP00000500994.1
CUL4B	ENST00000674073.2	n.*92_*95delCTTA		3_prime_UTR_variant	Exon 17 of 18			ENSP00000501262.2
CUL4B	ENST00000679405.1	n.*1745_*1748delCTTA		3_prime_UTR_variant	Exon 21 of 22			ENSP00000504985.1
CUL4B	ENST00000679432.1	n.*1745_*1748delCTTA		3_prime_UTR_variant	Exon 21 of 22			ENSP00000505343.1
CUL4B	ENST00000680918.1	n.*1452_*1455delCTTA		3_prime_UTR_variant	Exon 17 of 18			ENSP00000505955.1
CUL4B	ENST00000681080.1	n.*1745_*1748delCTTA		3_prime_UTR_variant	Exon 19 of 20			ENSP00000505898.1
CUL4B	ENST00000681189.1	n.*702_*705delCTTA		3_prime_UTR_variant	Exon 19 of 20			ENSP00000505973.1
CUL4B	ENST00000681333.1	n.*3429_*3432delCTTA		3_prime_UTR_variant	Exon 16 of 17			ENSP00000505739.1
CUL4B	ENST00000681908.1	n.*708_*711delCTTA		3_prime_UTR_variant	Exon 19 of 20			ENSP00000505777.1

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 Other:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Pathogenic:1

Oct 17, 2024

GeneDx

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Frameshift variant predicted to result in abnormal protein length as the last 50 amino acid(s) are replaced with 12 different amino acid(s), and other similar variants have been reported in HGMD; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 25385192) -

CUL4B-related disorder Other:1

-

GenomeConnect - Brain Gene Registry

Significance: not provided

Review Status: no classification provided

Collection Method: phenotyping only

Variant interpreted as Likely pathogenic and reported on 10-13-2018 by GeneDx. Assertions are reported exactly as they appear on the patient provided laboratory report. GenomeConnect does not attempt to reinterpret the variant. The IDDRC-CTSA National Brain Gene Registry (BGR) is a study funded by the U.S. National Center for Advancing Translational Sciences (NCATS) and includes 13 Intellectual and Developmental Disability Research Center (IDDRC) institutions. The study is led by Principal Investigator Philip Payne PhD, FACMI from Washington University. The BGR is a data commons of gene variants paired with subject clinical information. This database helps scientists learn more about genetic changes and their impact on the brain and behavior. Participation in the Brain Gene Registry requires participation in GenomeConnect. More information about the Brain Gene Registry can be found on the study website - https://braingeneregistry.wustl.edu/. -

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: rs1602567594; hg19: chrX-119664009;