chrX-120560261-TGAG-T

Variant names:

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP3BS2

The NM_001079872.2(CUL4B):c.375_377delCTC(p.Ser126del) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.0000816 in 1,176,913 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 14 hemizygotes in GnomAD. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.000045 ( 0 hom., 2 hem., cov: 22)

Exomes 𝑓: 0.000085 ( 0 hom. 12 hem. )

Consequence

CUL4B
NM_001079872.2 disruptive_inframe_deletion

Scores

Not classified

Clinical Significance

Likely benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 5.25

Variant links:

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 links:

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -5 ACMG points.

BP3

Nonframeshift variant in repetitive region in NM_001079872.2

BS2

High Hemizygotes in GnomAd4 at 2 XL gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CUL4B	NM_001079872.2 link	c.375_377delCTC	p.Ser126del	disruptive_inframe_deletion	Exon 1 of 20	ENST00000371322.11	NP_001073341.1	Q13620-1
CUL4B	NM_003588.4 link	c.429_431delCTC	p.Ser144del	disruptive_inframe_deletion	Exon 3 of 22		NP_003579.3	Q13620-2
CUL4B	NM_001330624.2 link	c.390_392delCTC	p.Ser131del	disruptive_inframe_deletion	Exon 2 of 21		NP_001317553.1	K4DI93

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
CUL4B	ENST00000371322.11 link	c.375_377delCTC	p.Ser126del	disruptive_inframe_deletion	Exon 1 of 20	1	NM_001079872.2	ENSP00000360373.5	Q13620-1
CUL4B	ENST00000681206.1 link	c.390_392delCTC	p.Ser131del	disruptive_inframe_deletion	Exon 2 of 23			ENSP00000505480.1	A0A7P0T954
CUL4B	ENST00000680673.1 link	c.429_431delCTC	p.Ser144del	disruptive_inframe_deletion	Exon 3 of 22			ENSP00000505084.1	Q13620-2
CUL4B	ENST00000681253.1 link	c.429_431delCTC	p.Ser144del	disruptive_inframe_deletion	Exon 4 of 23			ENSP00000506259.1	Q13620-2
CUL4B	ENST00000681652.1 link	c.429_431delCTC	p.Ser144del	disruptive_inframe_deletion	Exon 6 of 25			ENSP00000505176.1	Q13620-2
CUL4B	ENST00000336592.11 link	c.390_392delCTC	p.Ser131del	disruptive_inframe_deletion	Exon 2 of 21	5		ENSP00000338919.6	K4DI93
CUL4B	ENST00000674137.11 link	c.375_377delCTC	p.Ser126del	disruptive_inframe_deletion	Exon 1 of 20			ENSP00000501019.6	A0A669KAX4
CUL4B	ENST00000681090.1 link	c.375_377delCTC	p.Ser126del	disruptive_inframe_deletion	Exon 1 of 20			ENSP00000506288.1	A0A7P0TAQ3
CUL4B	ENST00000404115.8 link	c.375_377delCTC	p.Ser126del	disruptive_inframe_deletion	Exon 1 of 19	1		ENSP00000384109.4	A0A804CL36
CUL4B	ENST00000679927.1 link	c.30_32delCTC	p.Ser11del	disruptive_inframe_deletion	Exon 2 of 21			ENSP00000505603.1	A0A7P0T9L3
CUL4B	ENST00000673919.1 link	n.375_377delCTC		non_coding_transcript_exon_variant	Exon 1 of 21			ENSP00000500994.1	A0A669KAU9
CUL4B	ENST00000679432.1 link	n.360_362delCTC		non_coding_transcript_exon_variant	Exon 1 of 22			ENSP00000505343.1	A0A7P0T8W4
CUL4B	ENST00000681333.1 link	n.375_377delCTC		non_coding_transcript_exon_variant	Exon 1 of 17			ENSP00000505739.1	A0A7P0T9R8

Frequencies

GnomAD3 genomes

AF:

0.0000451

AC:

AN:

110981

Hom.:

Cov.:

AF XY:

0.0000600

AC XY:

AN XY:

33321

show subpopulations

Gnomad AFR

AF:

0.0000655

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0000959

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:

0.0000378

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.0000520

AC:

AN:

173145

Hom.:

AF XY:

0.0000162

AC XY:

AN XY:

61627

show subpopulations

Gnomad AFR exome

AF:

0.0000795

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.000340

Gnomad NFE exome

AF:

0.0000385

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.0000854

AC:

AN:

1065932

Hom.:

AF XY:

0.0000345

AC XY:

AN XY:

347582

show subpopulations

Gnomad4 AFR exome

AF:

0.0000777

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.0000340

Gnomad4 SAS exome

AF:

0.0000769

Gnomad4 FIN exome

AF:

0.0000761

Gnomad4 NFE exome

AF:

0.0000930

Gnomad4 OTH exome

AF:

0.000112

GnomAD4 genome

AF:

0.0000451

AC:

AN:

110981

Hom.:

Cov.:

AF XY:

0.0000600

AC XY:

AN XY:

33321

show subpopulations

Gnomad4 AFR

AF:

0.0000655

Gnomad4 AMR

AF:

0.0000959

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000378

Gnomad4 OTH

AF:

0.00

Asia WGS

AF:

0.00438

AC:

AN:

2522

ClinVar

Significance: Likely benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

X-linked intellectual disability Cabezas type

Benign:1

Apr 22, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

CUL4B-related disorder

Benign:1

Mar 16, 2021

PreventionGenetics, part of Exact Sciences

Significance: Likely benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

not provided

Benign:1

May 07, 2021

GeneDx

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over