X-120530171-C-G

Position:

• chrX-120530171-C-G

Variant summary

Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PM2 PP2 PP3_Strong

The NM_001079872.2(CUL4B):​c.2523G>C​(p.Lys841Asn) variant causes a missense change involving the alteration of a non-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 Uncertain significance (★).

• Frequency: Genomes: not found (cov: 23)
• Consequence: CUL4B NM_001079872.2 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 2.40

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 7 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP2: Missense variant in gene, where missense usually causes diseases (based on misZ statistic), CUL4B. . Gene score misZ 3.7714 (greater than the threshold 3.09). GenCC has associacion of gene with X-linked intellectual disability, Cabezas type.
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.953

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CUL4B	NM_001079872.2	c.2523G>C	p.Lys841Asn	missense_variant	19/20	ENST00000371322.11	NP_001073341.1
CUL4B	NM_003588.4	c.2577G>C	p.Lys859Asn	missense_variant	21/22		NP_003579.3
CUL4B	NM_001330624.2	c.2538G>C	p.Lys846Asn	missense_variant	20/21		NP_001317553.1
CUL4B	NM_001369145.1	c.1989G>C	p.Lys663Asn	missense_variant	19/20		NP_001356074.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CUL4B	ENST00000371322.11	c.2523G>C	p.Lys841Asn	missense_variant	19/20	1	NM_001079872.2	ENSP00000360373.5
CUL4B	ENST00000681206.1	c.2637G>C	p.Lys879Asn	missense_variant	22/23			ENSP00000505480.1
CUL4B	ENST00000680673.1	c.2577G>C	p.Lys859Asn	missense_variant	21/22			ENSP00000505084.1
CUL4B	ENST00000681253.1	c.2577G>C	p.Lys859Asn	missense_variant	22/23			ENSP00000506259.1
CUL4B	ENST00000681652.1	c.2577G>C	p.Lys859Asn	missense_variant	24/25			ENSP00000505176.1
CUL4B	ENST00000336592.11	c.2538G>C	p.Lys846Asn	missense_variant	20/21	5		ENSP00000338919.6
CUL4B	ENST00000674137.11	c.2529G>C	p.Lys843Asn	missense_variant	19/20			ENSP00000501019.6
CUL4B	ENST00000681090.1	c.2430G>C	p.Lys810Asn	missense_variant	19/20			ENSP00000506288.1
CUL4B	ENST00000679927.1	c.2178G>C	p.Lys726Asn	missense_variant	20/21			ENSP00000505603.1
CUL4B	ENST00000371323.3	c.1989G>C	p.Lys663Asn	missense_variant	19/20	5		ENSP00000360374.3
CUL4B	ENST00000680474.1	c.1965G>C	p.Lys655Asn	missense_variant	18/20			ENSP00000505562.1
CUL4B	ENST00000679844.1	c.1860G>C	p.Lys620Asn	missense_variant	17/18			ENSP00000505239.1
CUL4B	ENST00000404115.8	c.2439+2251G>C		intron_variant		1		ENSP00000384109.4
CUL4B	ENST00000673919.1	n.*1970G>C		non_coding_transcript_exon_variant	20/21			ENSP00000500994.1
CUL4B	ENST00000674073.2	n.*79G>C		non_coding_transcript_exon_variant	17/18			ENSP00000501262.2
CUL4B	ENST00000679405.1	n.*1732G>C		non_coding_transcript_exon_variant	21/22			ENSP00000504985.1
CUL4B	ENST00000679432.1	n.*1732G>C		non_coding_transcript_exon_variant	21/22			ENSP00000505343.1
CUL4B	ENST00000680918.1	n.*1439G>C		non_coding_transcript_exon_variant	17/18			ENSP00000505955.1
CUL4B	ENST00000681080.1	n.*1732G>C		non_coding_transcript_exon_variant	19/20			ENSP00000505898.1
CUL4B	ENST00000681189.1	n.*689G>C		non_coding_transcript_exon_variant	19/20			ENSP00000505973.1
CUL4B	ENST00000681333.1	n.*3416G>C		non_coding_transcript_exon_variant	16/17			ENSP00000505739.1
CUL4B	ENST00000681908.1	n.*695G>C		non_coding_transcript_exon_variant	19/20			ENSP00000505777.1
CUL4B	ENST00000673919.1	n.*1970G>C		3_prime_UTR_variant	20/21			ENSP00000500994.1
CUL4B	ENST00000674073.2	n.*79G>C		3_prime_UTR_variant	17/18			ENSP00000501262.2
CUL4B	ENST00000679405.1	n.*1732G>C		3_prime_UTR_variant	21/22			ENSP00000504985.1
CUL4B	ENST00000679432.1	n.*1732G>C		3_prime_UTR_variant	21/22			ENSP00000505343.1
CUL4B	ENST00000680918.1	n.*1439G>C		3_prime_UTR_variant	17/18			ENSP00000505955.1
CUL4B	ENST00000681080.1	n.*1732G>C		3_prime_UTR_variant	19/20			ENSP00000505898.1
CUL4B	ENST00000681189.1	n.*689G>C		3_prime_UTR_variant	19/20			ENSP00000505973.1
CUL4B	ENST00000681333.1	n.*3416G>C		3_prime_UTR_variant	16/17			ENSP00000505739.1
CUL4B	ENST00000681908.1	n.*695G>C		3_prime_UTR_variant	19/20			ENSP00000505777.1

Frequencies

GnomAD3 genomes Cov.: 23

GnomAD4 exome Cov.: 29

GnomAD4 genome Cov.: 23

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

X-linked intellectual disability Cabezas type Uncertain:1

Uncertain significance, criteria provided, single submitter

research

HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology

Sep 14, 2017

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	1.0
BayesDel_addAF	Pathogenic	0.33	D
BayesDel_noAF	Pathogenic	0.23
CADD	Uncertain	25
DANN	Uncertain	1.0
DEOGEN2	Pathogenic	0.82	.;.;D
FATHMM_MKL	Uncertain	0.95	D
LIST_S2	Pathogenic	1.0	D;D;D
M_CAP	Pathogenic	0.64	D
MetaRNN	Pathogenic	0.95	D;D;D
MetaSVM	Pathogenic	0.86	D
MutationAssessor	Pathogenic	4.4	.;.;H
PrimateAI	Pathogenic	0.91	D
PROVEAN	Pathogenic	-4.7	D;D;D
REVEL	Pathogenic	0.81
Sift	Pathogenic	0.0	D;D;D
Sift4G	Pathogenic	0.0	D;D;D
Polyphen		1.0	D;.;D
Vest4		0.89
MutPred		0.78		.;.;Gain of catalytic residue at M858 (P = 0.0226);
MVP		0.99
MPC		3.2
ClinPred		1.0	D
GERP RS		3.5
Varity_R		0.98
gMVP		0.98

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs1556181426; hg19: chrX-119664026;