rs573639761

Variant summary

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

The NM_001109763.2(GSG1L):​c.245C>T​(p.Pro82Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000848 in 1,179,288 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts 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. P82R) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 8.5e-7 ( 0 hom. )

Consequence

GSG1L
NM_001109763.2 missense

Scores

1
4
14

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0170
Variant links:
Genes affected
GSG1L (HGNC:28283): (GSG1 like) Predicted to be involved in regulation of AMPA receptor activity. Predicted to be located in postsynaptic density. Predicted to be active in Schaffer collateral - CA1 synapse; glutamatergic synapse; and plasma membrane. Predicted to be integral component of postsynaptic density membrane. [provided by Alliance of Genome Resources, Apr 2022]

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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=0.18915927).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
GSG1LNM_001109763.2 linkc.245C>T p.Pro82Leu missense_variant Exon 1 of 7 ENST00000447459.7 NP_001103233.1 Q6UXU4-1B3KY67

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
GSG1LENST00000447459.7 linkc.245C>T p.Pro82Leu missense_variant Exon 1 of 7 2 NM_001109763.2 ENSP00000394954.2 Q6UXU4-1
GSG1LENST00000395724.7 linkc.245C>T p.Pro82Leu missense_variant Exon 1 of 6 1 ENSP00000379074.3 Q6UXU4-3
GSG1LENST00000562611.1 linkn.8C>T non_coding_transcript_exon_variant Exon 1 of 7 3 ENSP00000454942.1 H3BNP0

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
AF:
8.48e-7
AC:
1
AN:
1179288
Hom.:
0
Cov.:
31
AF XY:
0.00000173
AC XY:
1
AN XY:
576368
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:
0.00000103
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.096
BayesDel_addAF
Benign
-0.17
T
BayesDel_noAF
Benign
-0.49
CADD
Benign
22
DANN
Uncertain
0.99
DEOGEN2
Benign
0.021
T;.
Eigen
Benign
-0.20
Eigen_PC
Benign
-0.24
FATHMM_MKL
Benign
0.61
D
LIST_S2
Benign
0.59
T;T
M_CAP
Uncertain
0.28
D
MetaRNN
Benign
0.19
T;T
MetaSVM
Benign
-1.1
T
MutationAssessor
Benign
1.4
L;L
PrimateAI
Pathogenic
0.80
D
PROVEAN
Benign
-1.4
N;N
REVEL
Benign
0.035
Sift
Uncertain
0.0070
D;D
Sift4G
Uncertain
0.024
D;D
Polyphen
0.61
P;P
Vest4
0.11
MutPred
0.42
Loss of glycosylation at P82 (P = 0.0063);Loss of glycosylation at P82 (P = 0.0063);
MVP
0.23
MPC
0.65
ClinPred
0.75
D
GERP RS
0.88
Varity_R
0.088
gMVP
0.24

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr16-28074501; API