NM_032806.6:c.1630C>T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_032806.6(POMGNT2):​c.1630C>T​(p.His544Tyr) variant causes a missense change. The variant allele was found at a frequency of 0.00000137 in 1,461,850 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. 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. H544D) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 33)
Exomes 𝑓: 0.0000014 ( 0 hom. )

Consequence

POMGNT2
NM_032806.6 missense

Scores

3
16

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 6.18
Variant links:
Genes affected
POMGNT2 (HGNC:25902): (protein O-linked mannose N-acetylglucosaminyltransferase 2 (beta 1,4-)) This gene encodes a protein with glycosyltransferase activity although its function is not currently known. [provided by RefSeq, Sep 2012]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.10417166).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
POMGNT2NM_032806.6 linkc.1630C>T p.His544Tyr missense_variant Exon 2 of 2 ENST00000344697.3 NP_116195.2 Q8NAT1A0A024R2P4
POMGNT2XM_005265515.4 linkc.1630C>T p.His544Tyr missense_variant Exon 3 of 3 XP_005265572.1 Q8NAT1A0A024R2P4
POMGNT2XM_011534163.3 linkc.1630C>T p.His544Tyr missense_variant Exon 3 of 3 XP_011532465.1 Q8NAT1A0A024R2P4
POMGNT2XM_017007353.2 linkc.1630C>T p.His544Tyr missense_variant Exon 4 of 4 XP_016862842.1 Q8NAT1A0A024R2P4

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
POMGNT2ENST00000344697.3 linkc.1630C>T p.His544Tyr missense_variant Exon 2 of 2 1 NM_032806.6 ENSP00000344125.2 Q8NAT1

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
AF:
0.00000137
AC:
2
AN:
1461850
Hom.:
0
Cov.:
29
AF XY:
0.00000138
AC XY:
1
AN XY:
727236
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000504
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.076
BayesDel_addAF
Benign
-0.17
T
BayesDel_noAF
Benign
-0.48
CADD
Benign
21
DANN
Benign
0.66
DEOGEN2
Benign
0.0095
T;T
Eigen
Benign
-0.13
Eigen_PC
Benign
0.13
FATHMM_MKL
Uncertain
0.95
D
LIST_S2
Uncertain
0.89
.;D
M_CAP
Benign
0.0039
T
MetaRNN
Benign
0.10
T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
0.77
N;N
PrimateAI
Uncertain
0.73
T
PROVEAN
Benign
0.020
N;N
REVEL
Benign
0.042
Sift
Benign
0.73
T;T
Sift4G
Benign
1.0
T;T
Polyphen
0.0010
B;B
Vest4
0.14
MutPred
0.44
Loss of glycosylation at T547 (P = 0.0309);Loss of glycosylation at T547 (P = 0.0309);
MVP
0.49
MPC
0.30
ClinPred
0.43
T
GERP RS
5.6
Varity_R
0.087
gMVP
0.61

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
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: rs2089829509; hg19: chr3-43121294; API