11-118349850-G-T

Variant summary

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

The NM_000073.3(CD3G):​c.187G>T​(p.Gly63Cys) 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. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 31)

Consequence

CD3G
NM_000073.3 missense

Scores

3
16

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.868
Variant links:
Genes affected
CD3G (HGNC:1675): (CD3 gamma subunit of T-cell receptor complex) The protein encoded by this gene is the CD3-gamma polypeptide, which together with CD3-epsilon, -delta and -zeta, and the T-cell receptor alpha/beta and gamma/delta heterodimers, forms the T-cell receptor-CD3 complex. This complex plays an important role in coupling antigen recognition to several intracellular signal-transduction pathways. The genes encoding the epsilon, gamma and delta polypeptides are located in the same cluster on chromosome 11. Defects in this gene are associated with T cell immunodeficiency. [provided by RefSeq, Jul 2008]

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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=0.08019915).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CD3GNM_000073.3 linkc.187G>T p.Gly63Cys missense_variant Exon 3 of 7 ENST00000532917.3 NP_000064.1 P09693B0YIY5
CD3GXM_005271724.5 linkc.187G>T p.Gly63Cys missense_variant Exon 3 of 4 XP_005271781.1
CD3GXM_006718941.4 linkc.187G>T p.Gly63Cys missense_variant Exon 3 of 7 XP_006719004.1 P09693B0YIY5

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CD3GENST00000532917.3 linkc.187G>T p.Gly63Cys missense_variant Exon 3 of 7 1 NM_000073.3 ENSP00000431445.2 P09693

Frequencies

GnomAD3 genomes
Cov.:
31
GnomAD3 exomes
AF:
0.00000398
AC:
1
AN:
251406
Hom.:
0
AF XY:
0.00000736
AC XY:
1
AN XY:
135874
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.0000544
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
Cov.:
31
GnomAD4 genome
Cov.:
31
ExAC
AF:
0.00000824
AC:
1

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.31
BayesDel_addAF
Benign
-0.28
T
BayesDel_noAF
Benign
-0.47
CADD
Benign
1.2
DANN
Benign
0.85
DEOGEN2
Uncertain
0.55
.;D;.
Eigen
Benign
-1.5
Eigen_PC
Benign
-1.5
FATHMM_MKL
Benign
0.012
N
LIST_S2
Benign
0.35
T;T;.
M_CAP
Benign
0.022
T
MetaRNN
Benign
0.080
T;T;T
MetaSVM
Benign
-0.98
T
MutationAssessor
Benign
0.46
.;N;.
PrimateAI
Benign
0.28
T
PROVEAN
Uncertain
-2.6
D;D;.
REVEL
Benign
0.11
Sift
Benign
0.11
T;D;.
Sift4G
Uncertain
0.0060
D;T;.
Polyphen
0.0
.;B;.
Vest4
0.23
MutPred
0.49
.;Loss of ubiquitination at K60 (P = 0.0768);.;
MVP
0.24
MPC
0.36
ClinPred
0.052
T
GERP RS
-5.4
Varity_R
0.51
gMVP
0.47

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: rs755334490; hg19: chr11-118220565; API