rs752855109

Variant summary

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

The NM_199286.4(DPPA3):​c.440C>G​(p.Ala147Gly) 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. 13/21 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. A147V) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 31)

Consequence

DPPA3
NM_199286.4 missense

Scores

1
3
15

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.910
Variant links:
Genes affected
DPPA3 (HGNC:19199): (developmental pluripotency associated 3) This gene encodes a protein that in mice may function as a maternal factor during the preimplantation stage of development. In mice, this gene may play a role in transcriptional repression, cell division, and maintenance of cell pluripotentiality. In humans, related intronless loci are located on chromosomes 14 and X. [provided by RefSeq, Jul 2008]

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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=0.17452884).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
DPPA3NM_199286.4 linkc.440C>G p.Ala147Gly missense_variant Exon 4 of 4 ENST00000345088.3 NP_954980.1 Q6W0C5

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
DPPA3ENST00000345088.3 linkc.440C>G p.Ala147Gly missense_variant Exon 4 of 4 1 NM_199286.4 ENSP00000339250.2 Q6W0C5

Frequencies

GnomAD3 genomes
Cov.:
31
GnomAD4 exome
Cov.:
31
GnomAD4 genome
Cov.:
31
Bravo
AF:
0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.27
BayesDel_addAF
Benign
-0.23
T
BayesDel_noAF
Benign
-0.57
CADD
Benign
15
DANN
Uncertain
0.98
DEOGEN2
Benign
0.25
T
Eigen
Benign
-0.65
Eigen_PC
Benign
-0.88
FATHMM_MKL
Benign
0.016
N
LIST_S2
Benign
0.49
T
M_CAP
Benign
0.0039
T
MetaRNN
Benign
0.17
T
MetaSVM
Benign
-1.0
T
MutationAssessor
Uncertain
2.0
M
PrimateAI
Benign
0.25
T
PROVEAN
Benign
-1.1
N
REVEL
Benign
0.063
Sift
Uncertain
0.019
D
Sift4G
Pathogenic
0.0
D
Polyphen
0.97
D
Vest4
0.15
MVP
0.24
MPC
0.50
ClinPred
0.57
D
GERP RS
-0.63
Varity_R
0.11
gMVP
0.012

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs752855109; hg19: chr12-7869633; API