rs782792216

Variant summary

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

The NM_001032382.2(PQBP1):​c.541C>G​(p.Arg181Gly) 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.

Frequency

Genomes: not found (cov: 22)

Consequence

PQBP1
NM_001032382.2 missense

Scores

2
6
9

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0300
Variant links:
Genes affected
PQBP1 (HGNC:9330): (polyglutamine binding protein 1) This gene encodes a nuclear polyglutamine-binding protein that is involved with transcription activation. The encoded protein contains a WW domain. Mutations in this gene have been found in patients with Renpenning syndrome 1 and other syndromes with X-linked cognitive disability. Multiple alternatively spliced transcript variants that encode different protein isoforms have been described for this gene.[provided by RefSeq, Nov 2009]

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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=0.34688532).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
PQBP1NM_001032382.2 linkc.541C>G p.Arg181Gly missense_variant Exon 5 of 7 ENST00000447146.7 NP_001027554.1 O60828-1A0A0S2Z4V5

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
PQBP1ENST00000447146.7 linkc.541C>G p.Arg181Gly missense_variant Exon 5 of 7 1 NM_001032382.2 ENSP00000391759.2 O60828-1

Frequencies

GnomAD3 genomes
Cov.:
22
GnomAD4 exome
Cov.:
35
GnomAD4 genome
Cov.:
22

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.89
BayesDel_addAF
Benign
0.0095
T
BayesDel_noAF
Benign
-0.22
CADD
Benign
22
DANN
Uncertain
1.0
DEOGEN2
Benign
0.25
T;T;T;T;.
FATHMM_MKL
Uncertain
0.83
D
LIST_S2
Uncertain
0.87
D;.;.;.;.
M_CAP
Pathogenic
0.77
D
MetaRNN
Benign
0.35
T;T;T;T;T
MetaSVM
Benign
-0.37
T
MutationAssessor
Benign
1.5
L;L;L;L;.
PrimateAI
Uncertain
0.60
T
PROVEAN
Benign
-1.8
N;N;N;N;N
REVEL
Uncertain
0.42
Sift
Uncertain
0.0040
D;D;D;D;D
Sift4G
Benign
0.15
T;T;T;T;T
Polyphen
0.99
D;D;D;D;.
Vest4
0.32
MutPred
0.24
Loss of helix (P = 0.0123);Loss of helix (P = 0.0123);Loss of helix (P = 0.0123);Loss of helix (P = 0.0123);Loss of helix (P = 0.0123);
MVP
0.79
MPC
1.9
ClinPred
0.95
D
GERP RS
-1.7
Varity_R
0.27

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
Details are displayed if max score is > 0.2

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: chrX-48759758; API