GeneBe

rs950597000

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_019845.3(RPRM):​c.316G>T​(p.Val106Leu) 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. 14/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V106M) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 33)

Consequence

RPRM
NM_019845.3 missense

Scores

2
16

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.56

Publications

0 publications found
Variant links:
Genes affected
RPRM (HGNC:24201): (reprimo, TP53 dependent G2 arrest mediator homolog) Predicted to be involved in regulation of mitotic cell cycle. Predicted to act upstream of or within regulation of cell cycle. Predicted to be integral component of membrane. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]
GALNT13 (HGNC:23242): (polypeptide N-acetylgalactosaminyltransferase 13) The GALNT13 protein is a member of the UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase (GalNAcT; EC 2.4.1.41) family, which initiate O-linked glycosylation of mucins (see MUC3A, MIM 158371) by the initial transfer of N-acetylgalactosamine (GalNAc) with an alpha-linkage to a serine or threonine residue.[supplied by OMIM, Apr 2004]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.1280899).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_019845.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
RPRM
NM_019845.3
MANE Select
c.316G>Tp.Val106Leu
missense
Exon 1 of 1NP_062819.1Q9NS64
GALNT13
NM_001422879.1
c.-327-24C>A
intron
N/ANP_001409808.1
GALNT13
NM_001422880.1
c.-327-24C>A
intron
N/ANP_001409809.1Q8IUC8-1

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
RPRM
ENST00000325926.4
TSL:6 MANE Select
c.316G>Tp.Val106Leu
missense
Exon 1 of 1ENSP00000314946.3Q9NS64
ENSG00000227400
ENST00000424322.1
TSL:4
n.430-56287G>T
intron
N/A
ENSG00000301085
ENST00000776049.1
n.177-24C>A
intron
N/A

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Cov.:
32
GnomAD4 genome
Cov.:
33
Alfa
AF:
0.00
Hom.:
0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.30
BayesDel_addAF
Benign
-0.010
T
BayesDel_noAF
Benign
-0.25
CADD
Uncertain
24
DANN
Benign
0.95
DEOGEN2
Benign
0.094
T
Eigen
Benign
0.086
Eigen_PC
Benign
0.19
FATHMM_MKL
Uncertain
0.92
D
LIST_S2
Benign
0.71
T
M_CAP
Benign
0.0091
T
MetaRNN
Benign
0.13
T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
0.69
N
PhyloP100
2.6
PrimateAI
Uncertain
0.63
T
PROVEAN
Benign
0.12
N
REVEL
Benign
0.15
Sift
Benign
0.66
T
Sift4G
Benign
0.64
T
Polyphen
0.71
P
Vest4
0.28
MutPred
0.14
Loss of sheet (P = 0.0817)
MVP
0.10
MPC
1.6
ClinPred
0.92
D
GERP RS
4.8
Varity_R
0.43
gMVP
0.72
Mutation Taster
=76/24
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: rs950597000; hg19: chr2-154334764; API