X-120526797-A-C
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_001079872.2(CUL4B):āc.2652T>Gā(p.Asp884Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000184 in 1,084,035 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 hemizygotes in GnomAD. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001079872.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CUL4B | NM_001079872.2 | c.2652T>G | p.Asp884Glu | missense_variant | Exon 20 of 20 | ENST00000371322.11 | NP_001073341.1 | |
CUL4B | NM_003588.4 | c.2706T>G | p.Asp902Glu | missense_variant | Exon 22 of 22 | NP_003579.3 | ||
CUL4B | NM_001330624.2 | c.2667T>G | p.Asp889Glu | missense_variant | Exon 21 of 21 | NP_001317553.1 | ||
CUL4B | NM_001369145.1 | c.2118T>G | p.Asp706Glu | missense_variant | Exon 20 of 20 | NP_001356074.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CUL4B | ENST00000371322.11 | c.2652T>G | p.Asp884Glu | missense_variant | Exon 20 of 20 | 1 | NM_001079872.2 | ENSP00000360373.5 | ||
CUL4B | ENST00000681206.1 | c.2766T>G | p.Asp922Glu | missense_variant | Exon 23 of 23 | ENSP00000505480.1 | ||||
CUL4B | ENST00000680673.1 | c.2706T>G | p.Asp902Glu | missense_variant | Exon 22 of 22 | ENSP00000505084.1 | ||||
CUL4B | ENST00000681253.1 | c.2706T>G | p.Asp902Glu | missense_variant | Exon 23 of 23 | ENSP00000506259.1 | ||||
CUL4B | ENST00000681652.1 | c.2706T>G | p.Asp902Glu | missense_variant | Exon 25 of 25 | ENSP00000505176.1 | ||||
CUL4B | ENST00000336592.11 | c.2667T>G | p.Asp889Glu | missense_variant | Exon 21 of 21 | 5 | ENSP00000338919.6 | |||
CUL4B | ENST00000674137.11 | c.2658T>G | p.Asp886Glu | missense_variant | Exon 20 of 20 | ENSP00000501019.6 | ||||
CUL4B | ENST00000681090.1 | c.2559T>G | p.Asp853Glu | missense_variant | Exon 20 of 20 | ENSP00000506288.1 | ||||
CUL4B | ENST00000404115.8 | c.2499T>G | p.Asp833Glu | missense_variant | Exon 19 of 19 | 1 | ENSP00000384109.4 | |||
CUL4B | ENST00000679927.1 | c.2307T>G | p.Asp769Glu | missense_variant | Exon 21 of 21 | ENSP00000505603.1 | ||||
CUL4B | ENST00000371323.3 | c.2118T>G | p.Asp706Glu | missense_variant | Exon 20 of 20 | 5 | ENSP00000360374.3 | |||
CUL4B | ENST00000679844.1 | c.1989T>G | p.Asp663Glu | missense_variant | Exon 18 of 18 | ENSP00000505239.1 | ||||
CUL4B | ENST00000680474 | c.*98T>G | 3_prime_UTR_variant | Exon 20 of 20 | ENSP00000505562.1 | |||||
CUL4B | ENST00000673919.1 | n.*2099T>G | non_coding_transcript_exon_variant | Exon 21 of 21 | ENSP00000500994.1 | |||||
CUL4B | ENST00000674073.2 | n.*208T>G | non_coding_transcript_exon_variant | Exon 18 of 18 | ENSP00000501262.2 | |||||
CUL4B | ENST00000679405.1 | n.*1861T>G | non_coding_transcript_exon_variant | Exon 22 of 22 | ENSP00000504985.1 | |||||
CUL4B | ENST00000679432.1 | n.*1861T>G | non_coding_transcript_exon_variant | Exon 22 of 22 | ENSP00000505343.1 | |||||
CUL4B | ENST00000680918.1 | n.*1568T>G | non_coding_transcript_exon_variant | Exon 18 of 18 | ENSP00000505955.1 | |||||
CUL4B | ENST00000681080.1 | n.*1861T>G | non_coding_transcript_exon_variant | Exon 20 of 20 | ENSP00000505898.1 | |||||
CUL4B | ENST00000681189.1 | n.*818T>G | non_coding_transcript_exon_variant | Exon 20 of 20 | ENSP00000505973.1 | |||||
CUL4B | ENST00000681333.1 | n.*3545T>G | non_coding_transcript_exon_variant | Exon 17 of 17 | ENSP00000505739.1 | |||||
CUL4B | ENST00000681908.1 | n.*824T>G | non_coding_transcript_exon_variant | Exon 20 of 20 | ENSP00000505777.1 | |||||
CUL4B | ENST00000673919.1 | n.*2099T>G | 3_prime_UTR_variant | Exon 21 of 21 | ENSP00000500994.1 | |||||
CUL4B | ENST00000674073.2 | n.*208T>G | 3_prime_UTR_variant | Exon 18 of 18 | ENSP00000501262.2 | |||||
CUL4B | ENST00000679405.1 | n.*1861T>G | 3_prime_UTR_variant | Exon 22 of 22 | ENSP00000504985.1 | |||||
CUL4B | ENST00000679432.1 | n.*1861T>G | 3_prime_UTR_variant | Exon 22 of 22 | ENSP00000505343.1 | |||||
CUL4B | ENST00000680918.1 | n.*1568T>G | 3_prime_UTR_variant | Exon 18 of 18 | ENSP00000505955.1 | |||||
CUL4B | ENST00000681080.1 | n.*1861T>G | 3_prime_UTR_variant | Exon 20 of 20 | ENSP00000505898.1 | |||||
CUL4B | ENST00000681189.1 | n.*818T>G | 3_prime_UTR_variant | Exon 20 of 20 | ENSP00000505973.1 | |||||
CUL4B | ENST00000681333.1 | n.*3545T>G | 3_prime_UTR_variant | Exon 17 of 17 | ENSP00000505739.1 | |||||
CUL4B | ENST00000681908.1 | n.*824T>G | 3_prime_UTR_variant | Exon 20 of 20 | ENSP00000505777.1 |
Frequencies
GnomAD3 genomes Cov.: 23
GnomAD3 exomes AF: 0.0000109 AC: 2AN: 183050Hom.: 0 AF XY: 0.0000148 AC XY: 1AN XY: 67578
GnomAD4 exome AF: 0.00000184 AC: 2AN: 1084035Hom.: 0 Cov.: 26 AF XY: 0.00000285 AC XY: 1AN XY: 351197
GnomAD4 genome Cov.: 23
ClinVar
Submissions by phenotype
X-linked intellectual disability Cabezas type Uncertain:1
Based on allele frequency, in-silico prediction scores and a certain overlap with the clinical phenotype, we interpreted this variant at least as of uncertain significance. The lack of one or more of the following features has discouraged further investigations: lack of a possible second hit in autosomal recessive conditions, presence of healthy controls in databases for autosomal dominant conditions, presence of unmatching cardinal clinical features in the patient or in the known gene-disease association, and/or variant type outside the known gene mutational spectrum. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at