17-7196492-G-C
Variant names:
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001321075.3(DLG4):c.1167C>G(p.Ile389Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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.
Frequency
Genomes: not found (cov: 32)
Consequence
DLG4
NM_001321075.3 missense
NM_001321075.3 missense
Scores
6
13
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.74
Genes affected
DLG4 (HGNC:2903): (discs large MAGUK scaffold protein 4) This gene encodes a member of the membrane-associated guanylate kinase (MAGUK) family. It heteromultimerizes with another MAGUK protein, DLG2, and is recruited into NMDA receptor and potassium channel clusters. These two MAGUK proteins 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. [provided by RefSeq, Jul 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
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DLG4 | ENST00000399506.9 | c.1167C>G | p.Ile389Met | missense_variant | Exon 10 of 20 | 2 | NM_001321075.3 | ENSP00000382425.2 | ||
DLG4 | ENST00000648172.8 | c.1296C>G | p.Ile432Met | missense_variant | Exon 12 of 22 | ENSP00000497806.3 | ||||
DLG4 | ENST00000648896.1 | c.1266C>G | p.Ile422Met | missense_variant | Exon 10 of 20 | ENSP00000497546.1 | ||||
DLG4 | ENST00000649520.1 | c.987C>G | p.Ile329Met | missense_variant | Exon 9 of 19 | ENSP00000497647.1 | ||||
DLG4 | ENST00000648263.1 | c.987C>G | p.Ile329Met | missense_variant | Exon 8 of 14 | ENSP00000498035.1 | ||||
DLG4 | ENST00000491753.2 | n.1296C>G | non_coding_transcript_exon_variant | Exon 12 of 21 | 2 | ENSP00000467897.2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Cov.: 39
GnomAD4 exome
Cov.:
39
GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
.;.;T;T;T;.;T;.;.;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Uncertain
D;D;D;.;D;D;D;D;D;D
M_CAP
Benign
T
MetaRNN
Uncertain
T;T;T;T;T;T;T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
.;.;L;.;.;.;.;.;.;.
PrimateAI
Uncertain
T
PROVEAN
Benign
.;N;N;.;.;.;.;.;.;.
REVEL
Benign
Sift
Uncertain
.;D;D;.;.;.;.;.;.;.
Sift4G
Uncertain
.;D;D;.;.;.;.;.;.;.
Polyphen
P;.;P;.;P;.;.;.;.;.
Vest4
0.42, 0.42
MutPred
0.46
.;.;Loss of methylation at K393 (P = 0.1106);.;.;.;.;.;.;.;
MVP
0.80
MPC
2.3
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at