chr17-42403374-C-A
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_012232.6(CAVIN1):c.*1313G>T 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. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 31)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
CAVIN1
NM_012232.6 3_prime_UTR
NM_012232.6 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.226
Publications
0 publications found
Genes affected
CAVIN1 (HGNC:9688): (caveolae associated protein 1) This gene encodes a protein that enables the dissociation of paused ternary polymerase I transcription complexes from the 3' end of pre-rRNA transcripts. This protein regulates rRNA transcription by promoting the dissociation of transcription complexes and the reinitiation of polymerase I on nascent rRNA transcripts. This protein also localizes to caveolae at the plasma membrane and is thought to play a critical role in the formation of caveolae and the stabilization of caveolins. This protein translocates from caveolae to the cytoplasm after insulin stimulation. Caveolae contain truncated forms of this protein and may be the site of phosphorylation-dependent proteolysis. This protein is also thought to modify lipid metabolism and insulin-regulated gene expression. Mutations in this gene result in a disorder characterized by generalized lipodystrophy and muscular dystrophy. [provided by RefSeq, Nov 2009]
CAVIN1 Gene-Disease associations (from GenCC):
- lipodystrophyInheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
- congenital generalized lipodystrophy type 4Inheritance: AR Classification: STRONG Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae)
- Berardinelli-Seip congenital lipodystrophyInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
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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=-0.47).
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_012232.6. You can select a different transcript below to see updated ACMG assignments.
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
31
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 866Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 566
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
866
Hom.:
Cov.:
0
AF XY:
AC XY:
0
AN XY:
566
African (AFR)
AF:
AC:
0
AN:
8
American (AMR)
AF:
AC:
0
AN:
4
Ashkenazi Jewish (ASJ)
AC:
0
AN:
0
East Asian (EAS)
AF:
AC:
0
AN:
150
South Asian (SAS)
AF:
AC:
0
AN:
10
European-Finnish (FIN)
AF:
AC:
0
AN:
426
Middle Eastern (MID)
AF:
AC:
0
AN:
4
European-Non Finnish (NFE)
AF:
AC:
0
AN:
244
Other (OTH)
AF:
AC:
0
AN:
20
GnomAD4 genome
GnomAD4 genome
Cov.:
31
ClinVar
ClinVar submissions
View on ClinVar Significance:Uncertain significance
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
1
-
Congenital generalized lipodystrophy type 4 (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
RBP_binding_hub_radar
RBP_regulation_power_radar
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
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