chr16-20319726-C-A

Variant summary

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

The NM_001502.4(GP2):​c.901G>T​(p.Val301Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts 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. V301I) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 33)

Consequence

GP2
NM_001502.4 missense

Scores

7
12

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.04
Variant links:
Genes affected
GP2 (HGNC:4441): (glycoprotein 2) This gene encodes an integral membrane protein that is secreted from intracellular zymogen granules and associates with the plasma membrane via glycosylphosphatidylinositol (GPI) linkage. The encoded protein binds pathogens such as enterobacteria, thereby playing an important role in the innate immune response. The C-terminus of this protein is related to the C-terminus of the protein encoded by the neighboring gene, uromodulin (UMOD). Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2015]

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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
GP2NM_001502.4 linkc.901G>T p.Val301Phe missense_variant Exon 6 of 11 ENST00000302555.10 NP_001493.2 P55259-3Q68D34B7Z1G2
GP2NM_001007240.3 linkc.910G>T p.Val304Phe missense_variant Exon 7 of 12 NP_001007241.2 P55259-1B7Z1G2
GP2NM_001007241.3 linkc.469G>T p.Val157Phe missense_variant Exon 6 of 11 NP_001007242.2 B7Z1G2
GP2NM_001007242.3 linkc.460G>T p.Val154Phe missense_variant Exon 5 of 10 NP_001007243.2 B7Z1G2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
GP2ENST00000302555.10 linkc.901G>T p.Val301Phe missense_variant Exon 6 of 11 1 NM_001502.4 ENSP00000304044.6 P55259-3

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Cov.:
29
GnomAD4 genome
Cov.:
33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.13
BayesDel_addAF
Benign
0.0072
T
BayesDel_noAF
Benign
-0.23
CADD
Uncertain
23
DANN
Uncertain
1.0
DEOGEN2
Benign
0.33
.;.;T;.
Eigen
Uncertain
0.21
Eigen_PC
Benign
0.12
FATHMM_MKL
Benign
0.51
D
LIST_S2
Benign
0.70
T;T;T;T
M_CAP
Benign
0.051
D
MetaRNN
Benign
0.33
T;T;T;T
MetaSVM
Uncertain
-0.23
T
MutationAssessor
Uncertain
2.2
.;.;M;.
PrimateAI
Benign
0.37
T
PROVEAN
Benign
-1.7
N;N;N;N
REVEL
Uncertain
0.48
Sift
Uncertain
0.0070
D;D;D;D
Sift4G
Uncertain
0.016
D;D;D;D
Polyphen
0.96
D;P;P;.
Vest4
0.19
MutPred
0.65
.;.;Gain of sheet (P = 0.1208);.;
MVP
0.71
MPC
0.20
ClinPred
0.65
D
GERP RS
3.3
Varity_R
0.15
gMVP
0.35

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.29
Details are displayed if max score is > 0.2
DS_AG_spliceai
0.29
Position offset: -20

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: rs201741257; hg19: chr16-20331048; API