rs1598494114

Variant names:

• chr17-40264931-C-G
• rs1598494114
• NM_133264.5:c.755C>G

Your query was ambiguous. Multiple possible variants found:

• chr17-40264931-C-G
• chr17-40264931-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_133264.5(WIPF2):​c.755C>G​(p.Pro252Arg) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. 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. P252L) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 31)
• Consequence: WIPF2 NM_133264.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.86

Genes affected

WIPF2 (HGNC:30923): (WAS/WASL interacting protein family member 2) This gene encodes a WASP interacting protein (WIP)-related protein. It has been shown that this protein has a role in the WASP-mediated organization of the actin cytoskeleton and that this protein is a potential link between the activated platelet-derived growth factor receptor and the actin polymerization machinery. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WIPF2	NM_133264.5	c.755C>G	p.Pro252Arg	missense_variant	Exon 5 of 8	ENST00000323571.9	NP_573571.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
WIPF2	ENST00000323571.9	c.755C>G	p.Pro252Arg	missense_variant	Exon 5 of 8	1	NM_133264.5	ENSP00000320924.4

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.70
BayesDel_addAF	Benign	-0.015	T
BayesDel_noAF	Benign	-0.26
CADD	Pathogenic	27
DANN	Uncertain	1.0
DEOGEN2	Benign	0.33	T;T;T
Eigen	Pathogenic	0.77
Eigen_PC	Pathogenic	0.76
FATHMM_MKL	Pathogenic	1.0	D
LIST_S2	Benign	0.84	.;.;T
M_CAP	Benign	0.050	D
MetaRNN	Uncertain	0.64	D;D;D
MetaSVM	Benign	-0.65	T
MutationAssessor	Uncertain	2.5	M;M;M
PrimateAI	Uncertain	0.72	T
PROVEAN	Uncertain	-4.1	D;.;.
REVEL	Uncertain	0.30
Sift	Pathogenic	0.0	D;.;.
Sift4G	Uncertain	0.0090	D;D;D
Polyphen		1.0	D;D;D
Vest4		0.63
MutPred		0.28		Loss of glycosylation at P252 (P = 0.0027);Loss of glycosylation at P252 (P = 0.0027);Loss of glycosylation at P252 (P = 0.0027);
MVP		0.72
MPC		0.66
ClinPred		0.99	D
GERP RS		5.7
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.69
gMVP		0.37

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

Other links and lift over

dbSNP: rs1598494114; hg19: chr17-38421183;