chr11-8101952-G-C
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_177972.3(TUB):c.*333G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
TUB
NM_177972.3 3_prime_UTR
NM_177972.3 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 3.44
Publications
11 publications found
Genes affected
TUB (HGNC:12406): (TUB bipartite transcription factor) This gene encodes a member of the Tubby family of bipartite transcription factors. The encoded protein may play a role in obesity and sensorineural degradation. The crystal structure has been determined for a similar protein in mouse, and it functions as a membrane-bound transcription regulator that translocates to the nucleus in response to phosphoinositide hydrolysis. Two transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]
RIC3 (HGNC:30338): (RIC3 acetylcholine receptor chaperone) This gene encodes a member of the resistance to inhibitors of cholinesterase 3-like family which functions as a chaperone of specific 5-hydroxytryptamine type 3 receptor and nicotinic acetylcholine receptor subtypes. The encoded protein influences the folding and assembly of these receptor subunits in the endoplasmic reticulum and expression on the cell surface. This protein contains an N-terminal transmembrane domain, a proline-rich spacer, and a cytosolic C-terminal coiled-coil domain. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2016]
RIC3 Gene-Disease associations (from GenCC):
- Parkinson diseaseInheritance: AD Classification: LIMITED Submitted by: Ambry Genetics
- movement disorderInheritance: AR Classification: LIMITED Submitted by: Ambry Genetics
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.78).
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TUB | ENST00000299506.3 | c.*333G>C | 3_prime_UTR_variant | Exon 12 of 12 | 1 | NM_177972.3 | ENSP00000299506.3 | |||
TUB | ENST00000305253.8 | c.*333G>C | 3_prime_UTR_variant | Exon 13 of 13 | 1 | ENSP00000305426.4 | ||||
TUB | ENST00000534099.5 | c.*333G>C | downstream_gene_variant | 2 | ENSP00000434400.1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 genomes
Cov.:
33
GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 173796Hom.: 0 Cov.: 3 AF XY: 0.00 AC XY: 0AN XY: 89164
GnomAD4 exome
Data not reliable, filtered out with message: AC0;AS_VQSR
AF:
AC:
0
AN:
173796
Hom.:
Cov.:
3
AF XY:
AC XY:
0
AN XY:
89164
African (AFR)
AF:
AC:
0
AN:
6464
American (AMR)
AF:
AC:
0
AN:
7512
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
5286
East Asian (EAS)
AF:
AC:
0
AN:
11662
South Asian (SAS)
AF:
AC:
0
AN:
14032
European-Finnish (FIN)
AF:
AC:
0
AN:
11052
Middle Eastern (MID)
AF:
AC:
0
AN:
826
European-Non Finnish (NFE)
AF:
AC:
0
AN:
106468
Other (OTH)
AF:
AC:
0
AN:
10494
GnomAD4 genome Cov.: 33
GnomAD4 genome
Cov.:
33
Alfa
AF:
Hom.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
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.