X-120560261-TGAGGAGGAG-TGAG
Variant summary
Our verdict is Likely benign. The variant received -5 ACMG points: 0P and 5B. BP3BS2
The NM_001079872.2(CUL4B):c.372_377delCTCCTC(p.Ser125_Ser126del) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.00000456 in 1,097,166 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 2 hemizygotes in GnomAD. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 22)
Exomes 𝑓: 0.0000046 ( 0 hom. 2 hem. )
Consequence
CUL4B
NM_001079872.2 disruptive_inframe_deletion
NM_001079872.2 disruptive_inframe_deletion
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 7.04
Publications
1 publications found
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 Gene-Disease associations (from GenCC):
- X-linked intellectual disability, Cabezas typeInheritance: XL Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), ClinGen, Orphanet, G2P
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -5 ACMG points.
BP3
Nonframeshift variant in repetitive region in NM_001079872.2
BS2
High Hemizygotes in GnomAdExome4 at 2 XL gene
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| CUL4B | NM_001079872.2 | c.372_377delCTCCTC | p.Ser125_Ser126del | disruptive_inframe_deletion | Exon 1 of 20 | ENST00000371322.11 | NP_001073341.1 | |
| CUL4B | NM_003588.4 | c.426_431delCTCCTC | p.Ser143_Ser144del | disruptive_inframe_deletion | Exon 3 of 22 | NP_003579.3 | ||
| CUL4B | NM_001330624.2 | c.387_392delCTCCTC | p.Ser130_Ser131del | disruptive_inframe_deletion | Exon 2 of 21 | NP_001317553.1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| CUL4B | ENST00000371322.11 | c.372_377delCTCCTC | p.Ser125_Ser126del | disruptive_inframe_deletion | Exon 1 of 20 | 1 | NM_001079872.2 | ENSP00000360373.5 | ||
| CUL4B | ENST00000681206.1 | c.387_392delCTCCTC | p.Ser130_Ser131del | disruptive_inframe_deletion | Exon 2 of 23 | ENSP00000505480.1 | ||||
| CUL4B | ENST00000680673.1 | c.426_431delCTCCTC | p.Ser143_Ser144del | disruptive_inframe_deletion | Exon 3 of 22 | ENSP00000505084.1 | ||||
| CUL4B | ENST00000681253.1 | c.426_431delCTCCTC | p.Ser143_Ser144del | disruptive_inframe_deletion | Exon 4 of 23 | ENSP00000506259.1 | ||||
| CUL4B | ENST00000681652.1 | c.426_431delCTCCTC | p.Ser143_Ser144del | disruptive_inframe_deletion | Exon 6 of 25 | ENSP00000505176.1 | ||||
| CUL4B | ENST00000336592.11 | c.387_392delCTCCTC | p.Ser130_Ser131del | disruptive_inframe_deletion | Exon 2 of 21 | 5 | ENSP00000338919.6 | |||
| CUL4B | ENST00000674137.11 | c.372_377delCTCCTC | p.Ser125_Ser126del | disruptive_inframe_deletion | Exon 1 of 20 | ENSP00000501019.6 | ||||
| CUL4B | ENST00000681090.1 | c.372_377delCTCCTC | p.Ser125_Ser126del | disruptive_inframe_deletion | Exon 1 of 20 | ENSP00000506288.1 | ||||
| CUL4B | ENST00000404115.8 | c.372_377delCTCCTC | p.Ser125_Ser126del | disruptive_inframe_deletion | Exon 1 of 19 | 1 | ENSP00000384109.4 | |||
| CUL4B | ENST00000679927.1 | c.27_32delCTCCTC | p.Ser10_Ser11del | disruptive_inframe_deletion | Exon 2 of 21 | ENSP00000505603.1 | ||||
| CUL4B | ENST00000673919.1 | n.372_377delCTCCTC | non_coding_transcript_exon_variant | Exon 1 of 21 | ENSP00000500994.1 | |||||
| CUL4B | ENST00000679432.1 | n.357_362delCTCCTC | non_coding_transcript_exon_variant | Exon 1 of 22 | ENSP00000505343.1 | |||||
| CUL4B | ENST00000681333.1 | n.372_377delCTCCTC | non_coding_transcript_exon_variant | Exon 1 of 17 | ENSP00000505739.1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
22
GnomAD2 exomes AF: 0.0000116 AC: 2AN: 173145 AF XY: 0.00 show subpopulations
GnomAD2 exomes
AF:
AC:
2
AN:
173145
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.00000456 AC: 5AN: 1097166Hom.: 0 AF XY: 0.00000551 AC XY: 2AN XY: 362892 show subpopulations
GnomAD4 exome
AF:
AC:
5
AN:
1097166
Hom.:
AF XY:
AC XY:
2
AN XY:
362892
show subpopulations
African (AFR)
AF:
AC:
0
AN:
26380
American (AMR)
AF:
AC:
2
AN:
35197
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
19371
East Asian (EAS)
AF:
AC:
0
AN:
30195
South Asian (SAS)
AF:
AC:
2
AN:
54099
European-Finnish (FIN)
AF:
AC:
0
AN:
40448
Middle Eastern (MID)
AF:
AC:
0
AN:
4133
European-Non Finnish (NFE)
AF:
AC:
1
AN:
841277
Other (OTH)
AF:
AC:
0
AN:
46066
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.458
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
GnomAD4 genome
Cov.:
22
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.