GeneBe

rs746495829

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 1 ACMG points: 2P and 1B. PM2BP4

The NM_004711.5(SYNGR1):​c.331G>T​(p.Val111Phe) 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. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 32)

Consequence

SYNGR1
NM_004711.5 missense

Scores

2
15

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 2.74

Publications

0 publications found
Variant links:
Genes affected
SYNGR1 (HGNC:11498): (synaptogyrin 1) This gene encodes an integral membrane protein associated with presynaptic vesicles in neuronal cells. The exact function of this protein is unclear, but studies of a similar murine protein suggest that it functions in synaptic plasticity without being required for synaptic transmission. The gene product belongs to the synaptogyrin gene family. Three alternatively spliced variants encoding three different isoforms have been identified. [provided by RefSeq, Jul 2008]
SYNGR1 Gene-Disease associations (from GenCC):
  • bipolar disorder
    Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics
  • schizophrenia
    Inheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.39018232).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004711.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
SYNGR1
NM_004711.5
MANE Select
c.331G>Tp.Val111Phe
missense
Exon 2 of 4NP_004702.2
SYNGR1
NM_145738.3
c.334G>Tp.Val112Phe
missense
Exon 2 of 4NP_663791.1O43759-3
SYNGR1
NM_145731.4
c.331G>Tp.Val111Phe
missense
Exon 2 of 4NP_663783.1O43759-2

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
SYNGR1
ENST00000328933.10
TSL:1 MANE Select
c.331G>Tp.Val111Phe
missense
Exon 2 of 4ENSP00000332287.5O43759-1
SYNGR1
ENST00000381535.4
TSL:1
c.334G>Tp.Val112Phe
missense
Exon 2 of 4ENSP00000370946.4O43759-3
SYNGR1
ENST00000318801.8
TSL:1
c.331G>Tp.Val111Phe
missense
Exon 2 of 4ENSP00000318845.4O43759-2

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
32
GnomAD4 genome
Cov.:
32

ClinVar

ClinVar submissions
Significance:Uncertain significance
Revision:criteria provided, single submitter
View on ClinVar
Pathogenic
VUS
Benign
Condition
-
1
-
not specified (1)

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.20
BayesDel_addAF
Benign
-0.11
T
BayesDel_noAF
Benign
-0.39
CADD
Benign
23
DANN
Benign
0.97
DEOGEN2
Benign
0.092
T
Eigen
Benign
-0.083
Eigen_PC
Benign
-0.066
FATHMM_MKL
Uncertain
0.88
D
LIST_S2
Uncertain
0.93
D
M_CAP
Benign
0.014
T
MetaRNN
Benign
0.39
T
MetaSVM
Benign
-1.1
T
MutationAssessor
Benign
0.56
N
PhyloP100
2.7
PROVEAN
Benign
2.0
N
REVEL
Benign
0.22
Sift
Benign
1.0
T
Sift4G
Benign
1.0
T
Polyphen
0.99
D
Vest4
0.56
MutPred
0.61
Loss of glycosylation at S107 (P = 0.1488)
MVP
0.31
MPC
0.64
ClinPred
0.87
D
GERP RS
3.1
Varity_R
0.073
gMVP
0.96
Mutation Taster
=66/34
polymorphism

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

Other links and lift over

dbSNP: rs746495829; hg19: chr22-39770552; API