X-120526781-G-A

Position:

• chrX-120526781-G-A

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.2668C>T​(p.Gln890*) variant causes a stop gained change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★).

• Frequency:
  • Genomes: not found (cov: 23)
  • Exomes 𝑓: 0.0 (0 hom. 0 hem.)
  • Failed GnomAD Quality Control
• Consequence: CUL4B NM_001079872.2 stop_gained
• Clinical Significance: Likely pathogenic criteria provided, single submitter P:1
• Conservation: PhyloP100: 9.60

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 exon, not predicted to undergo nonsense mediated mRNA decay. Fraction of 0.00744 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-120526781-G-A is Pathogenic according to our data. Variant chrX-120526781-G-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 633520.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CUL4B	NM_001079872.2	c.2668C>T	p.Gln890*	stop_gained	20/20	ENST00000371322.11	NP_001073341.1
CUL4B	NM_003588.4	c.2722C>T	p.Gln908*	stop_gained	22/22		NP_003579.3
CUL4B	NM_001330624.2	c.2683C>T	p.Gln895*	stop_gained	21/21		NP_001317553.1
CUL4B	NM_001369145.1	c.2134C>T	p.Gln712*	stop_gained	20/20		NP_001356074.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CUL4B	ENST00000371322.11	c.2668C>T	p.Gln890*	stop_gained	20/20	1	NM_001079872.2	ENSP00000360373.5
CUL4B	ENST00000681206.1	c.2782C>T	p.Gln928*	stop_gained	23/23			ENSP00000505480.1
CUL4B	ENST00000680673.1	c.2722C>T	p.Gln908*	stop_gained	22/22			ENSP00000505084.1
CUL4B	ENST00000681253.1	c.2722C>T	p.Gln908*	stop_gained	23/23			ENSP00000506259.1
CUL4B	ENST00000681652.1	c.2722C>T	p.Gln908*	stop_gained	25/25			ENSP00000505176.1
CUL4B	ENST00000336592.11	c.2683C>T	p.Gln895*	stop_gained	21/21	5		ENSP00000338919.6
CUL4B	ENST00000674137.11	c.2674C>T	p.Gln892*	stop_gained	20/20			ENSP00000501019.6
CUL4B	ENST00000681090.1	c.2575C>T	p.Gln859*	stop_gained	20/20			ENSP00000506288.1
CUL4B	ENST00000404115.8	c.2515C>T	p.Gln839*	stop_gained	19/19	1		ENSP00000384109.4
CUL4B	ENST00000679927.1	c.2323C>T	p.Gln775*	stop_gained	21/21			ENSP00000505603.1
CUL4B	ENST00000371323.3	c.2134C>T	p.Gln712*	stop_gained	20/20	5		ENSP00000360374.3
CUL4B	ENST00000679844.1	c.2005C>T	p.Gln669*	stop_gained	18/18			ENSP00000505239.1
CUL4B	ENST00000680474	c.*114C>T		3_prime_UTR_variant	20/20			ENSP00000505562.1
CUL4B	ENST00000673919.1	n.*2115C>T		non_coding_transcript_exon_variant	21/21			ENSP00000500994.1
CUL4B	ENST00000674073.2	n.*224C>T		non_coding_transcript_exon_variant	18/18			ENSP00000501262.2
CUL4B	ENST00000679405.1	n.*1877C>T		non_coding_transcript_exon_variant	22/22			ENSP00000504985.1
CUL4B	ENST00000679432.1	n.*1877C>T		non_coding_transcript_exon_variant	22/22			ENSP00000505343.1
CUL4B	ENST00000680918.1	n.*1584C>T		non_coding_transcript_exon_variant	18/18			ENSP00000505955.1
CUL4B	ENST00000681080.1	n.*1877C>T		non_coding_transcript_exon_variant	20/20			ENSP00000505898.1
CUL4B	ENST00000681189.1	n.*834C>T		non_coding_transcript_exon_variant	20/20			ENSP00000505973.1
CUL4B	ENST00000681333.1	n.*3561C>T		non_coding_transcript_exon_variant	17/17			ENSP00000505739.1
CUL4B	ENST00000681908.1	n.*840C>T		non_coding_transcript_exon_variant	20/20			ENSP00000505777.1
CUL4B	ENST00000673919.1	n.*2115C>T		3_prime_UTR_variant	21/21			ENSP00000500994.1
CUL4B	ENST00000674073.2	n.*224C>T		3_prime_UTR_variant	18/18			ENSP00000501262.2
CUL4B	ENST00000679405.1	n.*1877C>T		3_prime_UTR_variant	22/22			ENSP00000504985.1
CUL4B	ENST00000679432.1	n.*1877C>T		3_prime_UTR_variant	22/22			ENSP00000505343.1
CUL4B	ENST00000680918.1	n.*1584C>T		3_prime_UTR_variant	18/18			ENSP00000505955.1
CUL4B	ENST00000681080.1	n.*1877C>T		3_prime_UTR_variant	20/20			ENSP00000505898.1
CUL4B	ENST00000681189.1	n.*834C>T		3_prime_UTR_variant	20/20			ENSP00000505973.1
CUL4B	ENST00000681333.1	n.*3561C>T		3_prime_UTR_variant	17/17			ENSP00000505739.1
CUL4B	ENST00000681908.1	n.*840C>T		3_prime_UTR_variant	20/20			ENSP00000505777.1

Frequencies

GnomAD3 genomes Cov.: 23

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 1074426 Hom.: 0 Cov.: 25 AF XY: 0.00 AC XY: 0 AN XY: 343224

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 23

ClinVar

Significance: Likely pathogenic

Submissions summary: Pathogenic:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Laboratory of Molecular Genetics (Pr. Bezieau's lab), CHU de Nantes

Jun 28, 2018

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.62	D
BayesDel_noAF	Pathogenic	0.66
CADD	Pathogenic	37
DANN	Uncertain	1.0
FATHMM_MKL	Pathogenic	0.99	D
Vest4		0.62
GERP RS		5.7

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: rs1569385075; hg19: chrX-119660636;