20-37802979-A-G
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_030877.5(CTNNBL1):āc.1144A>Gā(p.Ile382Val) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000124 in 1,614,068 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: š 0.0000066 ( 0 hom., cov: 32)
Exomes š: 0.000013 ( 0 hom. )
Consequence
CTNNBL1
NM_030877.5 missense
NM_030877.5 missense
Scores
2
4
13
Clinical Significance
Conservation
PhyloP100: 9.21
Genes affected
CTNNBL1 (HGNC:15879): (catenin beta like 1) The protein encoded by this gene is a component of the pre-mRNA-processing factor 19-cell division cycle 5-like (PRP19-CDC5L) protein complex, which activates pre-mRNA splicing and is an integral part of the spliceosome. The encoded protein is also a nuclear localization sequence binding protein, and binds to activation-induced deaminase and is important for antibody diversification. This gene may also be associated with the development of obesity. Alternative splicing results in multiple transcript variants. A pseudogene of this gene has been defined on the X chromosome. [provided by RefSeq, Jul 2013]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CTNNBL1 | NM_030877.5 | c.1144A>G | p.Ile382Val | missense_variant | 11/16 | ENST00000361383.11 | NP_110517.2 | |
CTNNBL1 | NM_001281495.2 | c.1063A>G | p.Ile355Val | missense_variant | 12/17 | NP_001268424.1 | ||
CTNNBL1 | XM_024451947.2 | c.1063A>G | p.Ile355Val | missense_variant | 12/17 | XP_024307715.1 | ||
CTNNBL1 | XM_011528917.3 | c.814A>G | p.Ile272Val | missense_variant | 9/14 | XP_011527219.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CTNNBL1 | ENST00000361383.11 | c.1144A>G | p.Ile382Val | missense_variant | 11/16 | 1 | NM_030877.5 | ENSP00000355050.6 | ||
CTNNBL1 | ENST00000628103.2 | c.1063A>G | p.Ile355Val | missense_variant | 12/17 | 2 | ENSP00000487198.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152192Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251096Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135682
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GnomAD4 exome AF: 0.0000130 AC: 19AN: 1461876Hom.: 0 Cov.: 32 AF XY: 0.0000179 AC XY: 13AN XY: 727236
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GnomAD4 genome AF: 0.00000657 AC: 1AN: 152192Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74348
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 08, 2022 | The c.1144A>G (p.I382V) alteration is located in exon 11 (coding exon 11) of the CTNNBL1 gene. This alteration results from a A to G substitution at nucleotide position 1144, causing the isoleucine (I) at amino acid position 382 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
.;.;T;.;.;.
Eigen
Benign
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D;D;.;D;D
M_CAP
Benign
T
MetaRNN
Uncertain
T;T;T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
.;.;L;.;.;.
PrimateAI
Pathogenic
T
PROVEAN
Benign
.;N;N;.;N;N
REVEL
Benign
Sift
Benign
.;T;T;.;T;T
Sift4G
Benign
T;T;T;T;T;T
Polyphen
0.19, 0.20
.;.;B;.;B;.
Vest4
MutPred
0.60
.;.;Loss of helix (P = 0.079);.;.;.;
MVP
MPC
0.38
ClinPred
T
GERP RS
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gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at