chrX-120544122-C-A

Position:

• chrX-120544122-C-A

Variant summary

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

The NM_001079872.2(CUL4B):​c.1165G>T​(p.Glu389*) 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 Pathogenic (★). Variant results in nonsense mediated mRNA decay.

• Frequency: Genomes: not found (cov: 23)
• Consequence: CUL4B NM_001079872.2 stop_gained
• Clinical Significance: Pathogenic criteria provided, single submitter P:1
• Conservation: PhyloP100: 7.84

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 (HGNC:):

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-120544122-C-A is Pathogenic according to our data. Variant chrX-120544122-C-A is described in ClinVar as [Pathogenic]. Clinvar id is 521119.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.1165G>T	p.Glu389*	stop_gained	7/20	ENST00000371322.11	NP_001073341.1
CUL4B	NM_003588.4	c.1219G>T	p.Glu407*	stop_gained	9/22		NP_003579.3
CUL4B	NM_001330624.2	c.1180G>T	p.Glu394*	stop_gained	8/21		NP_001317553.1
CUL4B	NM_001369145.1	c.631G>T	p.Glu211*	stop_gained	7/20		NP_001356074.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CUL4B	ENST00000371322.11	c.1165G>T	p.Glu389*	stop_gained	7/20	1	NM_001079872.2	ENSP00000360373.5
CUL4B	ENST00000681206.1	c.1279G>T	p.Glu427*	stop_gained	10/23			ENSP00000505480.1
CUL4B	ENST00000680673.1	c.1219G>T	p.Glu407*	stop_gained	9/22			ENSP00000505084.1
CUL4B	ENST00000681253.1	c.1219G>T	p.Glu407*	stop_gained	10/23			ENSP00000506259.1
CUL4B	ENST00000681652.1	c.1219G>T	p.Glu407*	stop_gained	12/25			ENSP00000505176.1
CUL4B	ENST00000336592.11	c.1180G>T	p.Glu394*	stop_gained	8/21	5		ENSP00000338919.6
CUL4B	ENST00000674137.11	c.1165G>T	p.Glu389*	stop_gained	7/20			ENSP00000501019.6
CUL4B	ENST00000681090.1	c.1072G>T	p.Glu358*	stop_gained	7/20			ENSP00000506288.1
CUL4B	ENST00000404115.8	c.1165G>T	p.Glu389*	stop_gained	7/19	1		ENSP00000384109.4
CUL4B	ENST00000679927.1	c.820G>T	p.Glu274*	stop_gained	8/21			ENSP00000505603.1
CUL4B	ENST00000371323.3	c.631G>T	p.Glu211*	stop_gained	7/20	5		ENSP00000360374.3
CUL4B	ENST00000680474.1	c.607G>T	p.Glu203*	stop_gained	6/20			ENSP00000505562.1
CUL4B	ENST00000679844.1	c.607G>T	p.Glu203*	stop_gained	6/18			ENSP00000505239.1
CUL4B	ENST00000673919.1	n.*612G>T		non_coding_transcript_exon_variant	8/21			ENSP00000500994.1
CUL4B	ENST00000674073.2	n.607G>T		non_coding_transcript_exon_variant	6/18			ENSP00000501262.2
CUL4B	ENST00000679405.1	n.*374G>T		non_coding_transcript_exon_variant	9/22			ENSP00000504985.1
CUL4B	ENST00000679432.1	n.*374G>T		non_coding_transcript_exon_variant	9/22			ENSP00000505343.1
CUL4B	ENST00000680918.1	n.*81G>T		non_coding_transcript_exon_variant	5/18			ENSP00000505955.1
CUL4B	ENST00000681080.1	n.*374G>T		non_coding_transcript_exon_variant	7/20			ENSP00000505898.1
CUL4B	ENST00000681189.1	n.607G>T		non_coding_transcript_exon_variant	6/20			ENSP00000505973.1
CUL4B	ENST00000681333.1	n.1165G>T		non_coding_transcript_exon_variant	7/17			ENSP00000505739.1
CUL4B	ENST00000681869.1	n.607G>T		non_coding_transcript_exon_variant	6/17			ENSP00000505597.1
CUL4B	ENST00000681908.1	n.607G>T		non_coding_transcript_exon_variant	6/20			ENSP00000505777.1
CUL4B	ENST00000673919.1	n.*612G>T		3_prime_UTR_variant	8/21			ENSP00000500994.1
CUL4B	ENST00000679405.1	n.*374G>T		3_prime_UTR_variant	9/22			ENSP00000504985.1
CUL4B	ENST00000679432.1	n.*374G>T		3_prime_UTR_variant	9/22			ENSP00000505343.1
CUL4B	ENST00000680918.1	n.*81G>T		3_prime_UTR_variant	5/18			ENSP00000505955.1
CUL4B	ENST00000681080.1	n.*374G>T		3_prime_UTR_variant	7/20			ENSP00000505898.1

Frequencies

GnomAD3 genomes Cov.: 23

GnomAD4 exome Cov.: 24

GnomAD4 genome Cov.: 23

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: criteria provided, single submitter

Submissions by phenotype

Inborn genetic diseases Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Jun 01, 2016

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.67	D
BayesDel_noAF	Pathogenic	0.66
CADD	Pathogenic	36
DANN	Uncertain	1.0
FATHMM_MKL	Pathogenic	0.99	D
Vest4		0.87
GERP RS		5.7
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7

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: rs1556213001; hg19: chrX-119677977;