rs724159976
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PVS1PM2PP5
The NM_020461.4(TUBGCP6):c.3565G>T(p.Gly1189Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 32)
Consequence
TUBGCP6
NM_020461.4 stop_gained
NM_020461.4 stop_gained
Scores
2
2
3
Clinical Significance
Conservation
PhyloP100: 2.82
Genes affected
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 11 ACMG points.
PVS1
?
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PM2
?
Very rare variant in population databases, with high coverage;
PP5
?
Variant 22-50220794-C-A is Pathogenic according to our data. Variant chr22-50220794-C-A is described in ClinVar as [Pathogenic]. Clinvar id is 162405.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr22-50220794-C-A is described in Lovd as [Likely_pathogenic].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TUBGCP6 | NM_020461.4 | c.3565G>T | p.Gly1189Ter | stop_gained | 16/25 | ENST00000248846.10 | |
TUBGCP6 | XR_001755343.3 | n.4129G>T | non_coding_transcript_exon_variant | 16/20 | |||
TUBGCP6 | XR_938347.3 | n.4129G>T | non_coding_transcript_exon_variant | 16/23 | |||
TUBGCP6 | XR_007067982.1 | n.3049-779G>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TUBGCP6 | ENST00000248846.10 | c.3565G>T | p.Gly1189Ter | stop_gained | 16/25 | 1 | NM_020461.4 | P1 | |
TUBGCP6 | ENST00000439308.6 | c.3565G>T | p.Gly1189Ter | stop_gained | 16/25 | 1 | |||
TUBGCP6 | ENST00000498611.5 | n.3617+481G>T | intron_variant, non_coding_transcript_variant | 1 | |||||
TUBGCP6 | ENST00000491449.5 | n.1872G>T | non_coding_transcript_exon_variant | 8/16 | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
GnomAD4 exome Cov.: 39
GnomAD4 exome
Cov.:
39
GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Microcephaly and chorioretinopathy 1 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Dec 01, 2014 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
Cadd
Pathogenic
Dann
Benign
Eigen
Uncertain
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
MutationTaster
Benign
A;A
Vest4
GERP RS
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