rs368959516

Variant summary

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

The NM_001142699.3(DLG2):ā€‹c.2618G>Cā€‹(p.Arg873Thr) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.000000689 in 1,450,996 control chromosomes in the GnomAD database, with no homozygous occurrence. 2/3 splice prediction tools predicting alterations to normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 31)
Exomes š‘“: 6.9e-7 ( 0 hom. )

Consequence

DLG2
NM_001142699.3 missense, splice_region

Scores

3
8
8
Splicing: ADA: 0.9896
2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.79
Variant links:
Genes affected
DLG2 (HGNC:2901): (discs large MAGUK scaffold protein 2) This gene encodes a member of the membrane-associated guanylate kinase (MAGUK) family. The encoded protein forms a heterodimer with a related family member that may interact at postsynaptic sites to form a multimeric scaffold for the clustering of receptors, ion channels, and associated signaling proteins. Multiple transcript variants encoding different isoforms have been found for this gene. Additional transcript variants have been described, but their full-length nature is not known. [provided by RefSeq, Dec 2008]

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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
DLG2NM_001142699.3 linkc.2618G>C p.Arg873Thr missense_variant, splice_region_variant Exon 25 of 28 ENST00000376104.7 NP_001136171.1 Q15700-2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
DLG2ENST00000376104.7 linkc.2618G>C p.Arg873Thr missense_variant, splice_region_variant Exon 25 of 28 1 NM_001142699.3 ENSP00000365272.2 Q15700-2

Frequencies

GnomAD3 genomes
Cov.:
31
GnomAD3 exomes
AF:
0.00000413
AC:
1
AN:
242352
Hom.:
0
AF XY:
0.00000759
AC XY:
1
AN XY:
131690
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00000901
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
6.89e-7
AC:
1
AN:
1450996
Hom.:
0
Cov.:
32
AF XY:
0.00000139
AC XY:
1
AN XY:
721474
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
9.04e-7
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
31
Bravo
AF:
0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.83
BayesDel_addAF
Uncertain
0.14
D
BayesDel_noAF
Uncertain
-0.040
CADD
Pathogenic
33
DANN
Uncertain
0.98
DEOGEN2
Benign
0.29
.;T;.;.;.;.;.;T;T;T;T;.
Eigen
Uncertain
0.37
Eigen_PC
Uncertain
0.47
FATHMM_MKL
Pathogenic
0.99
D
LIST_S2
Uncertain
0.93
D;D;D;D;D;D;D;D;D;D;D;D
M_CAP
Benign
0.025
T
MetaRNN
Uncertain
0.47
T;T;T;T;T;T;T;T;T;T;T;T
MetaSVM
Benign
-1.1
T
MutationAssessor
Benign
0.93
.;L;.;.;.;.;.;.;.;.;.;.
PrimateAI
Pathogenic
0.86
D
PROVEAN
Uncertain
-3.4
D;D;D;.;.;D;D;D;D;D;D;D
REVEL
Benign
0.22
Sift
Benign
0.12
T;T;T;.;.;T;T;T;T;T;T;T
Sift4G
Benign
0.12
T;T;T;.;.;T;T;T;T;T;T;.
Polyphen
0.27, 0.96, 1.0, 0.060, 0.086, 0.98
.;B;.;.;.;D;D;B;B;D;D;.
Vest4
0.60
MutPred
0.40
.;Loss of MoRF binding (P = 0.0509);.;.;.;.;.;.;.;.;.;.;
MVP
0.79
MPC
2.0
ClinPred
0.91
D
GERP RS
5.7
Varity_R
0.43
gMVP
0.91

Splicing

Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Pathogenic
0.99
dbscSNV1_RF
Pathogenic
0.89
SpliceAI score (max)
0.090
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: rs368959516; hg19: chr11-83180245; API