rs543467029

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001384711.1(GLT8D2):​c.454G>C​(p.Val152Leu) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V152I) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 32)

Consequence

GLT8D2
NM_001384711.1 missense

Scores

10
9

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.96
Variant links:
Genes affected
GLT8D2 (HGNC:24890): (glycosyltransferase 8 domain containing 2) Predicted to enable glycosyltransferase activity. Predicted to be integral component of membrane. Predicted to be active in Golgi apparatus. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
GLT8D2NM_001384711.1 linkc.454G>C p.Val152Leu missense_variant Exon 7 of 11 ENST00000360814.9 NP_001371640.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
GLT8D2ENST00000360814.9 linkc.454G>C p.Val152Leu missense_variant Exon 7 of 11 1 NM_001384711.1 ENSP00000354053.4 Q9H1C3
GLT8D2ENST00000546436.5 linkc.454G>C p.Val152Leu missense_variant Exon 6 of 10 5 ENSP00000449750.1 Q9H1C3
GLT8D2ENST00000548660.5 linkc.454G>C p.Val152Leu missense_variant Exon 7 of 11 2 ENSP00000447450.1 Q9H1C3

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
29
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.49
BayesDel_addAF
Uncertain
0.014
T
BayesDel_noAF
Benign
-0.22
CADD
Uncertain
25
DANN
Uncertain
1.0
DEOGEN2
Benign
0.29
T;T;T
Eigen
Uncertain
0.56
Eigen_PC
Uncertain
0.59
FATHMM_MKL
Uncertain
0.93
D
LIST_S2
Uncertain
0.87
.;.;D
M_CAP
Benign
0.012
T
MetaRNN
Uncertain
0.57
D;D;D
MetaSVM
Benign
-0.99
T
MutationAssessor
Uncertain
2.4
M;M;M
PrimateAI
Uncertain
0.67
T
PROVEAN
Benign
-1.5
N;N;N
REVEL
Benign
0.16
Sift
Benign
0.18
T;T;T
Sift4G
Benign
0.26
T;T;T
Polyphen
0.96
D;D;D
Vest4
0.62
MutPred
0.58
Gain of catalytic residue at E150 (P = 0.0042);Gain of catalytic residue at E150 (P = 0.0042);Gain of catalytic residue at E150 (P = 0.0042);
MVP
0.36
MPC
0.38
ClinPred
0.91
D
GERP RS
5.4
Varity_R
0.27
gMVP
0.82

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs543467029; hg19: chr12-104391262; API