GeneBe

rs2034190485

Variant names:

Variant summary

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

The NM_002811.5(PSMD7):​c.914A>G​(p.Glu305Gly) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 13/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 33)

Consequence

PSMD7
NM_002811.5 missense

Scores

1
2
15

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 9.04

Publications

0 publications found
Variant links:
Genes affected
PSMD7 (HGNC:9565): (proteasome 26S subunit, non-ATPase 7) The 26S proteasome is a multicatalytic proteinase complex with a highly ordered structure composed of 2 complexes, a 20S core and a 19S regulator. The 20S core is composed of 4 rings of 28 non-identical subunits; 2 rings are composed of 7 alpha subunits and 2 rings are composed of 7 beta subunits. The 19S regulator is composed of a base, which contains 6 ATPase subunits and 2 non-ATPase subunits, and a lid, which contains up to 10 non-ATPase subunits. Proteasomes are distributed throughout eukaryotic cells at a high concentration and cleave peptides in an ATP/ubiquitin-dependent process in a non-lysosomal pathway. An essential function of a modified proteasome, the immunoproteasome, is the processing of class I MHC peptides. This gene encodes a non-ATPase subunit of the 19S regulator. A pseudogene has been identified on chromosome 17. [provided by RefSeq, Jul 2008]

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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=0.13450813).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002811.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
PSMD7
NM_002811.5
MANE Select
c.914A>Gp.Glu305Gly
missense
Exon 7 of 7NP_002802.2

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
PSMD7
ENST00000219313.9
TSL:1 MANE Select
c.914A>Gp.Glu305Gly
missense
Exon 7 of 7ENSP00000219313.4P51665
PSMD7
ENST00000937729.1
c.821A>Gp.Glu274Gly
missense
Exon 6 of 6ENSP00000607788.1
PSMD7
ENST00000937730.1
c.803A>Gp.Glu268Gly
missense
Exon 7 of 7ENSP00000607789.1

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Cov.:
30
GnomAD4 genome
Cov.:
33
Alfa
AF:
0.00
Hom.:
0

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
0.092
BayesDel_addAF
Benign
-0.024
T
BayesDel_noAF
Benign
-0.27
CADD
Uncertain
24
DANN
Uncertain
1.0
DEOGEN2
Benign
0.11
T
Eigen
Benign
-0.12
Eigen_PC
Benign
0.11
FATHMM_MKL
Pathogenic
0.97
D
LIST_S2
Benign
0.55
T
M_CAP
Benign
0.027
D
MetaRNN
Benign
0.13
T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
1.4
L
PhyloP100
9.0
PrimateAI
Uncertain
0.68
T
PROVEAN
Benign
-0.36
N
REVEL
Benign
0.13
Sift
Benign
0.21
T
Sift4G
Benign
0.17
T
Polyphen
0.010
B
Vest4
0.32
MutPred
0.21
Gain of loop (P = 0.0097)
MVP
0.60
MPC
0.53
ClinPred
0.72
D
GERP RS
5.0
Varity_R
0.12
gMVP
0.079

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: rs2034190485; hg19: chr16-74339570; API