chr1-183938858-G-A
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Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_015101.4(COLGALT2):c.1784C>T(p.Ser595Phe) variant causes a missense change. 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: 32)
Consequence
COLGALT2
NM_015101.4 missense
NM_015101.4 missense
Scores
1
11
6
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 6.11
Genes affected
COLGALT2 (HGNC:16790): (collagen beta(1-O)galactosyltransferase 2) Predicted to enable procollagen galactosyltransferase activity. Predicted to be involved in collagen fibril organization. Predicted to be located in endoplasmic reticulum lumen. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.3696711).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COLGALT2 | NM_015101.4 | c.1784C>T | p.Ser595Phe | missense_variant | 12/12 | ENST00000361927.9 | |
COLGALT2 | NM_001303421.2 | c.1424C>T | p.Ser475Phe | missense_variant | 12/12 | ||
COLGALT2 | NM_001303420.2 | c.1604+1723C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COLGALT2 | ENST00000361927.9 | c.1784C>T | p.Ser595Phe | missense_variant | 12/12 | 1 | NM_015101.4 | P1 | |
COLGALT2 | ENST00000367520.3 | c.995C>T | p.Ser332Phe | missense_variant | 7/7 | 2 | |||
COLGALT2 | ENST00000367521.5 | c.608C>T | p.Ser203Phe | missense_variant | 4/4 | 2 | |||
COLGALT2 | ENST00000649786.1 | c.1604+1723C>T | intron_variant |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Cov.: 33
GnomAD4 exome
Cov.:
33
GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Uncertain
D
BayesDel_noAF
Benign
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Benign
T;T;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D;D
M_CAP
Uncertain
D
MetaRNN
Benign
T;T;T
MetaSVM
Uncertain
T
MutationTaster
Benign
D;D;D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;N
REVEL
Uncertain
Sift
Uncertain
D;D;D
Sift4G
Uncertain
D;D;D
Polyphen
0.71, 0.58
.;P;P
Vest4
MutPred
0.33
.;Loss of disorder (P = 0.0117);.;
MVP
MPC
0.59
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.