rs777796155
Positions:
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_020461.4(TUBGCP6):āc.1529T>Gā(p.Leu510Arg) variant causes a missense change. The variant allele was found at a frequency of 0.00000943 in 1,590,208 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ā ).
Frequency
Genomes: š 0.0000066 ( 0 hom., cov: 32)
Exomes š: 0.0000097 ( 1 hom. )
Consequence
TUBGCP6
NM_020461.4 missense
NM_020461.4 missense
Scores
2
9
8
Clinical Significance
Conservation
PhyloP100: 6.66
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.823
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TUBGCP6 | NM_020461.4 | c.1529T>G | p.Leu510Arg | missense_variant | 7/25 | ENST00000248846.10 | |
TUBGCP6 | XR_001755343.3 | n.2093T>G | non_coding_transcript_exon_variant | 7/20 | |||
TUBGCP6 | XR_007067982.1 | n.2093T>G | non_coding_transcript_exon_variant | 7/19 | |||
TUBGCP6 | XR_938347.3 | n.2093T>G | non_coding_transcript_exon_variant | 7/23 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TUBGCP6 | ENST00000248846.10 | c.1529T>G | p.Leu510Arg | missense_variant | 7/25 | 1 | NM_020461.4 | P1 | |
TUBGCP6 | ENST00000439308.6 | c.1529T>G | p.Leu510Arg | missense_variant | 7/25 | 1 | |||
TUBGCP6 | ENST00000498611.5 | n.2062T>G | non_coding_transcript_exon_variant | 7/23 | 1 | ||||
TUBGCP6 | ENST00000434349.1 | c.761T>G | p.Leu254Arg | missense_variant | 6/6 | 5 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152176Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.00000953 AC: 2AN: 209886Hom.: 0 AF XY: 0.00000890 AC XY: 1AN XY: 112348
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GnomAD4 exome AF: 0.00000974 AC: 14AN: 1438032Hom.: 1 Cov.: 33 AF XY: 0.00000842 AC XY: 6AN XY: 712764
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GnomAD4 genome AF: 0.00000657 AC: 1AN: 152176Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74336
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Apr 02, 2015 | - - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Nov 13, 2023 | This sequence change replaces leucine, which is neutral and non-polar, with arginine, which is basic and polar, at codon 510 of the TUBGCP6 protein (p.Leu510Arg). This variant is present in population databases (rs777796155, gnomAD 0.004%). This variant has not been reported in the literature in individuals affected with TUBGCP6-related conditions. ClinVar contains an entry for this variant (Variation ID: 212506). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D
M_CAP
Benign
T
MetaRNN
Pathogenic
D;D
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;.
MutationTaster
Benign
D;D
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D;D
REVEL
Benign
Sift
Uncertain
D;D
Sift4G
Uncertain
D;D
Polyphen
D;.
Vest4
MutPred
Loss of stability (P = 0.0075);Loss of stability (P = 0.0075);
MVP
MPC
ClinPred
D
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
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