rs147254848

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4

The NM_152657.4(GGN):​c.1826G>T​(p.Arg609Leu) 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. 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. R609H) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 33)

Consequence

GGN
NM_152657.4 missense

Scores

1
8
10

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.221
Variant links:
Genes affected
GGN (HGNC:18869): (gametogenetin) This gene is a germ cell-specific gene that encodes proteins that interact with POG (proliferation of germ cells). Alternatively spliced transcript variants of a similar mouse gene encode at least three different proteins, namely gametogenetin protein 1a, gametogenetin protein 2, and gametogenetin protein 3, which show a perinuclear, cytoplasmic, and nucleolar localization, respectively. These proteins regulate the localization of POG and may play a role in spermatogenesis. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.37869567).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
GGNNM_152657.4 linkc.1826G>T p.Arg609Leu missense_variant Exon 3 of 4 ENST00000334928.11 NP_689870.3 Q86UU5-1
GGNXM_005258619.5 linkc.1826G>T p.Arg609Leu missense_variant Exon 3 of 4 XP_005258676.1 Q86UU5-1
GGNXM_017026451.2 linkc.1826G>T p.Arg609Leu missense_variant Exon 2 of 3 XP_016881940.1 Q86UU5-1
GGNXM_011526603.3 linkc.1577G>T p.Arg526Leu missense_variant Exon 3 of 4 XP_011524905.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
GGNENST00000334928.11 linkc.1826G>T p.Arg609Leu missense_variant Exon 3 of 4 1 NM_152657.4 ENSP00000334940.5 Q86UU5-1

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Cov.:
33
GnomAD4 genome
Cov.:
33
Bravo
AF:
0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.32
BayesDel_addAF
Uncertain
0.11
D
BayesDel_noAF
Uncertain
-0.070
CADD
Uncertain
24
DANN
Uncertain
1.0
DEOGEN2
Benign
0.14
T
Eigen
Uncertain
0.19
Eigen_PC
Benign
0.14
FATHMM_MKL
Benign
0.43
N
LIST_S2
Benign
0.56
T
M_CAP
Uncertain
0.090
D
MetaRNN
Benign
0.38
T
MetaSVM
Benign
-0.58
T
MutationAssessor
Benign
0.97
L
PrimateAI
Uncertain
0.65
T
PROVEAN
Uncertain
-3.4
D
REVEL
Benign
0.091
Sift
Uncertain
0.0080
D
Sift4G
Pathogenic
0.0
D
Polyphen
0.99
D
Vest4
0.48
MutPred
0.30
Loss of MoRF binding (P = 0.0059);
MVP
0.61
MPC
1.1
ClinPred
0.98
D
GERP RS
3.6
Varity_R
0.26
gMVP
0.36

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.050
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: rs147254848; hg19: chr19-38876076; API