rs285584

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001164595.2(PDZRN4):​c.1285G>A​(p.Gly429Ser) variant causes a missense change. The variant allele was found at a frequency of 0.163 in 1,611,684 control chromosomes in the GnomAD database, including 22,491 homozygotes. 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 nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.18 ( 2585 hom., cov: 32)
Exomes 𝑓: 0.16 ( 19906 hom. )

Consequence

PDZRN4
NM_001164595.2 missense

Scores

3
5
10

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 6.72
Variant links:
Genes affected
PDZRN4 (HGNC:30552): (PDZ domain containing ring finger 4) Predicted to enable metal ion binding activity. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.0017770231).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.237 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
PDZRN4NM_001164595.2 linkuse as main transcriptc.1285G>A p.Gly429Ser missense_variant 6/10 ENST00000402685.7
PDZRN4NM_013377.4 linkuse as main transcriptc.511G>A p.Gly171Ser missense_variant 4/8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
PDZRN4ENST00000402685.7 linkuse as main transcriptc.1285G>A p.Gly429Ser missense_variant 6/102 NM_001164595.2 P1Q6ZMN7-1

Frequencies

GnomAD3 genomes
AF:
0.181
AC:
27443
AN:
151850
Hom.:
2584
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.241
Gnomad AMI
AF:
0.105
Gnomad AMR
AF:
0.121
Gnomad ASJ
AF:
0.183
Gnomad EAS
AF:
0.0978
Gnomad SAS
AF:
0.173
Gnomad FIN
AF:
0.189
Gnomad MID
AF:
0.212
Gnomad NFE
AF:
0.164
Gnomad OTH
AF:
0.175
GnomAD3 exomes
AF:
0.158
AC:
39614
AN:
250912
Hom.:
3522
AF XY:
0.161
AC XY:
21879
AN XY:
135580
show subpopulations
Gnomad AFR exome
AF:
0.245
Gnomad AMR exome
AF:
0.0770
Gnomad ASJ exome
AF:
0.179
Gnomad EAS exome
AF:
0.0942
Gnomad SAS exome
AF:
0.176
Gnomad FIN exome
AF:
0.186
Gnomad NFE exome
AF:
0.168
Gnomad OTH exome
AF:
0.163
GnomAD4 exome
AF:
0.161
AC:
234743
AN:
1459714
Hom.:
19906
Cov.:
32
AF XY:
0.162
AC XY:
117904
AN XY:
726268
show subpopulations
Gnomad4 AFR exome
AF:
0.241
Gnomad4 AMR exome
AF:
0.0837
Gnomad4 ASJ exome
AF:
0.176
Gnomad4 EAS exome
AF:
0.107
Gnomad4 SAS exome
AF:
0.179
Gnomad4 FIN exome
AF:
0.189
Gnomad4 NFE exome
AF:
0.160
Gnomad4 OTH exome
AF:
0.163
GnomAD4 genome
AF:
0.181
AC:
27452
AN:
151970
Hom.:
2585
Cov.:
32
AF XY:
0.179
AC XY:
13305
AN XY:
74258
show subpopulations
Gnomad4 AFR
AF:
0.241
Gnomad4 AMR
AF:
0.121
Gnomad4 ASJ
AF:
0.183
Gnomad4 EAS
AF:
0.0974
Gnomad4 SAS
AF:
0.172
Gnomad4 FIN
AF:
0.189
Gnomad4 NFE
AF:
0.164
Gnomad4 OTH
AF:
0.173
Alfa
AF:
0.164
Hom.:
5436
Bravo
AF:
0.176
TwinsUK
AF:
0.152
AC:
562
ALSPAC
AF:
0.157
AC:
605
ESP6500AA
AF:
0.239
AC:
1055
ESP6500EA
AF:
0.161
AC:
1387
ExAC
AF:
0.165
AC:
20013
Asia WGS
AF:
0.141
AC:
495
AN:
3478
EpiCase
AF:
0.163
EpiControl
AF:
0.160

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.14
BayesDel_addAF
Benign
-0.35
T
BayesDel_noAF
Benign
-0.13
CADD
Uncertain
25
DANN
Pathogenic
1.0
DEOGEN2
Benign
0.050
T;.;.;.
Eigen
Pathogenic
0.72
Eigen_PC
Pathogenic
0.71
FATHMM_MKL
Uncertain
0.91
D
LIST_S2
Uncertain
0.87
D;D;D;D
MetaRNN
Benign
0.0018
T;T;T;T
MetaSVM
Benign
-1.2
T
MutationAssessor
Benign
1.6
L;.;.;.
MutationTaster
Benign
0.0000021
P;P;P
PrimateAI
Uncertain
0.60
T
PROVEAN
Uncertain
-4.3
D;.;D;D
REVEL
Uncertain
0.29
Sift
Benign
0.10
T;.;D;D
Sift4G
Benign
0.083
T;.;D;D
Polyphen
1.0
D;.;D;D
Vest4
0.27
MPC
0.41
ClinPred
0.019
T
GERP RS
5.0
Varity_R
0.58
gMVP
0.68

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: rs285584; hg19: chr12-41946539; COSMIC: COSV54194883; API