chr8-86402047-G-A

Variant summary

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

The NM_007013.4(WWP1):​c.568G>A​(p.Asp190Asn) variant causes a missense change. 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. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 33)

Consequence

WWP1
NM_007013.4 missense

Scores

1
1
17

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 6.75
Variant links:
Genes affected
WWP1 (HGNC:17004): (WW domain containing E3 ubiquitin protein ligase 1) WW domain-containing proteins are found in all eukaryotes and play an important role in the regulation of a wide variety of cellular functions such as protein degradation, transcription, and RNA splicing. This gene encodes a protein which contains 4 tandem WW domains and a HECT (homologous to the E6-associated protein carboxyl terminus) domain. The encoded protein belongs to a family of NEDD4-like proteins, which are E3 ubiquitin-ligase molecules and regulate key trafficking decisions, including targeting of proteins to proteosomes or lysosomes. Alternative splicing of this gene generates at least 6 transcript variants; however, the full length nature of these transcripts has not been defined. [provided by RefSeq, Jul 2008]

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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=0.26748145).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
WWP1NM_007013.4 linkuse as main transcriptc.568G>A p.Asp190Asn missense_variant 8/25 ENST00000517970.6 NP_008944.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
WWP1ENST00000517970.6 linkuse as main transcriptc.568G>A p.Asp190Asn missense_variant 8/251 NM_007013.4 ENSP00000427793 P1Q9H0M0-1
WWP1ENST00000265428.4 linkuse as main transcriptc.568G>A p.Asp190Asn missense_variant 6/231 ENSP00000265428 P1Q9H0M0-1
WWP1ENST00000518683.5 linkuse as main transcriptn.378+3409G>A intron_variant, non_coding_transcript_variant 1

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Cov.:
31
GnomAD4 genome
Cov.:
33

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsDec 18, 2023The c.568G>A (p.D190N) alteration is located in exon 8 (coding exon 6) of the WWP1 gene. This alteration results from a G to A substitution at nucleotide position 568, causing the aspartic acid (D) at amino acid position 190 to be replaced by an asparagine (N). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.067
BayesDel_addAF
Benign
-0.21
T
BayesDel_noAF
Benign
-0.54
CADD
Benign
22
DANN
Uncertain
0.99
DEOGEN2
Benign
0.12
T;T
Eigen
Benign
-0.16
Eigen_PC
Benign
0.028
FATHMM_MKL
Pathogenic
0.98
D
LIST_S2
Benign
0.77
.;T
M_CAP
Benign
0.015
T
MetaRNN
Benign
0.27
T;T
MetaSVM
Benign
-1.1
T
MutationAssessor
Benign
0.81
L;L
MutationTaster
Benign
1.0
D;D;D;D
PrimateAI
Benign
0.43
T
PROVEAN
Benign
-0.64
N;N
REVEL
Benign
0.060
Sift
Benign
0.31
T;T
Sift4G
Benign
0.26
T;T
Polyphen
0.010
B;B
Vest4
0.53
MutPred
0.24
Loss of catalytic residue at D190 (P = 0.094);Loss of catalytic residue at D190 (P = 0.094);
MVP
0.15
MPC
0.11
ClinPred
0.80
D
GERP RS
5.7
Varity_R
0.057
gMVP
0.30

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: rs1337176530; hg19: chr8-87414276; API