rs565369538

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4

The NM_002081.3(GPC1):​c.238C>G​(p.Arg80Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000205 in 1,460,436 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 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. R80C) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 33)
Exomes š‘“: 0.0000021 ( 0 hom. )

Consequence

GPC1
NM_002081.3 missense

Scores

4
15

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.144
Variant links:
Genes affected
GPC1 (HGNC:4449): (glypican 1) Cell surface heparan sulfate proteoglycans are composed of a membrane-associated protein core substituted with a variable number of heparan sulfate chains. Members of the glypican-related integral membrane proteoglycan family (GRIPS) contain a core protein anchored to the cytoplasmic membrane via a glycosyl phosphatidylinositol linkage. These proteins may play a role in the control of cell division and growth regulation. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

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=0.2797432).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
GPC1NM_002081.3 linkc.238C>G p.Arg80Gly missense_variant Exon 2 of 9 ENST00000264039.7 NP_002072.2 P35052-1A0A384NPH9
GPC1XM_047443961.1 linkc.22C>G p.Arg8Gly missense_variant Exon 2 of 9 XP_047299917.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
GPC1ENST00000264039.7 linkc.238C>G p.Arg80Gly missense_variant Exon 2 of 9 1 NM_002081.3 ENSP00000264039.2 P35052-1

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD3 exomes
AF:
0.00000403
AC:
1
AN:
248338
Hom.:
0
AF XY:
0.00000741
AC XY:
1
AN XY:
135012
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.0000290
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.00000205
AC:
3
AN:
1460436
Hom.:
0
Cov.:
31
AF XY:
0.00000138
AC XY:
1
AN XY:
726538
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.0000224
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
8.99e-7
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
0.15
BayesDel_addAF
Benign
-0.14
T
BayesDel_noAF
Benign
-0.35
CADD
Benign
22
DANN
Uncertain
0.99
DEOGEN2
Benign
0.38
T;T;.;.;T
Eigen
Benign
-0.23
Eigen_PC
Benign
-0.26
FATHMM_MKL
Benign
0.29
N
LIST_S2
Benign
0.76
T;T;T;T;T
M_CAP
Benign
0.029
D
MetaRNN
Benign
0.28
T;T;T;T;T
MetaSVM
Benign
-0.85
T
MutationAssessor
Uncertain
2.3
M;.;.;.;.
PrimateAI
Uncertain
0.61
T
PROVEAN
Uncertain
-3.9
D;N;D;.;.
REVEL
Benign
0.11
Sift
Benign
0.048
D;D;T;.;.
Sift4G
Benign
0.10
T;T;T;T;T
Polyphen
0.20
B;.;.;.;.
Vest4
0.43
MutPred
0.58
Loss of catalytic residue at R80 (P = 0.0665);.;.;.;.;
MVP
0.70
MPC
0.47
ClinPred
0.90
D
GERP RS
3.1
Varity_R
0.34
gMVP
0.41

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: rs565369538; hg19: chr2-241398518; API