13-45465160-T-C
Position:
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3PP5
The NM_031431.4(COG3):c.124T>C(p.Ser42Pro) variant causes a missense change. 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).
Frequency
Genomes: not found (cov: 33)
Consequence
COG3
NM_031431.4 missense
NM_031431.4 missense
Scores
3
7
9
Clinical Significance
Conservation
PhyloP100: 5.73
Genes affected
COG3 (HGNC:18619): (component of oligomeric golgi complex 3) This gene encodes a component of the conserved oligomeric Golgi (COG) complex which is composed of eight different subunits and is required for normal Golgi morphology and localization. Defects in the COG complex result in multiple deficiencies in protein glycosylation. The protein encoded by this gene is involved in ER-Golgi transport.[provided by RefSeq, Jun 2011]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.755
PP5
Variant 13-45465160-T-C is Pathogenic according to our data. Variant chr13-45465160-T-C is described in ClinVar as [Pathogenic]. Clinvar id is 2584759.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COG3 | NM_031431.4 | c.124T>C | p.Ser42Pro | missense_variant | 1/23 | ENST00000349995.10 | |
COG3 | XM_047430702.1 | c.124T>C | p.Ser42Pro | missense_variant | 1/19 | ||
COG3 | XR_007063702.1 | n.222T>C | non_coding_transcript_exon_variant | 1/14 | |||
COG3 | XR_429222.5 | n.222T>C | non_coding_transcript_exon_variant | 1/24 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COG3 | ENST00000349995.10 | c.124T>C | p.Ser42Pro | missense_variant | 1/23 | 1 | NM_031431.4 | P1 | |
COG3 | ENST00000617493.1 | c.124T>C | p.Ser42Pro | missense_variant | 1/12 | 1 | |||
COG3 | ENST00000476702.1 | c.97T>C | p.Ser33Pro | missense_variant | 1/2 | 3 | |||
COG3 | ENST00000617325.1 | n.263T>C | non_coding_transcript_exon_variant | 1/2 | 3 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 genomes
Cov.:
33
GnomAD4 exome Cov.: 30
GnomAD4 exome
Cov.:
30
GnomAD4 genome Cov.: 33
GnomAD4 genome
Cov.:
33
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Congenital disorder of glycosylation, type IIbb Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Oct 19, 2023 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Uncertain
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Benign
T;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Benign
D
LIST_S2
Benign
T;T
M_CAP
Uncertain
D
MetaRNN
Pathogenic
D;D
MetaSVM
Benign
T
MutationAssessor
Benign
L;L
MutationTaster
Benign
D
PrimateAI
Uncertain
T
PROVEAN
Uncertain
N;.
REVEL
Benign
Sift
Benign
T;.
Sift4G
Benign
T;D
Polyphen
D;D
Vest4
MutPred
Gain of loop (P = 3e-04);Gain of loop (P = 3e-04);
MVP
MPC
ClinPred
D
GERP RS
Varity_R
gMVP
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
No publications associated with this variant yet.