X-48688403-T-C

Position:

• chrX-48688403-T-C

Variant summary

Our verdict is Pathogenic. Variant got 14 ACMG points: 14P and 0B. PM2 PP3_Strong PP5_Very_Strong

The NM_000377.3(WAS):​c.881T>C​(p.Ile294Thr) 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 pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★).

• Frequency: Genomes: not found (cov: 23)
• Consequence: WAS NM_000377.3 missense
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:9
• Conservation: PhyloP100: 7.36

Genes affected

WAS (HGNC:12731): (WASP actin nucleation promoting factor) The Wiskott-Aldrich syndrome (WAS) family of proteins share similar domain structure, and are involved in transduction of signals from receptors on the cell surface to the actin cytoskeleton. The presence of a number of different motifs suggests that they are regulated by a number of different stimuli, and interact with multiple proteins. Recent studies have demonstrated that these proteins, directly or indirectly, associate with the small GTPase, Cdc42, known to regulate formation of actin filaments, and the cytoskeletal organizing complex, Arp2/3. Wiskott-Aldrich syndrome is a rare, inherited, X-linked, recessive disease characterized by immune dysregulation and microthrombocytopenia, and is caused by mutations in the WAS gene. The WAS gene product is a cytoplasmic protein, expressed exclusively in hematopoietic cells, which show signalling and cytoskeletal abnormalities in WAS patients. A transcript variant arising as a result of alternative promoter usage, and containing a different 5' UTR sequence, has been described, however, its full-length nature is not known. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Pathogenic. Variant got 14 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.984
• PP5: Variant X-48688403-T-C is Pathogenic according to our data. Variant chrX-48688403-T-C is described in ClinVar as [Likely_pathogenic]. Clinvar id is 29967.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
WAS	NM_000377.3	c.881T>C	p.Ile294Thr	missense_variant	9/12	ENST00000376701.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
WAS	ENST00000376701.5	c.881T>C	p.Ile294Thr	missense_variant	9/12	1	NM_000377.3	P2

Frequencies

GnomAD3 genomes Cov.: 23

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 23

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:9

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

X-linked severe congenital neutropenia Pathogenic:5

Pathogenic, criteria provided, single submitter	clinical testing	Genomics Facility, Ludwig-Maximilians-Universität München	Dec 28, 2021	- -
Pathogenic, no assertion criteria provided	literature only	OMIM	Jan 01, 2009	- -
Pathogenic, criteria provided, single submitter	clinical testing	Victorian Clinical Genetics Services, Murdoch Childrens Research Institute	Jul 17, 2023	Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0103 - Loss of function and gain of function are known mechanisms of disease in this gene and are associated with diseases. Loss of function is a known mechanism associated with X-linked thrombocytopenia (XLT; MIM#313900) and Wiskott-Aldrich syndrome (WAS; MIM#301000) (PMID: 12969986). While gain of function is shown to be associated with X-linked severe congenital neutropenia (MIM#300299) (PMIDs: 11242115, 20513746). (I) 0109 - This gene is associated with X-linked recessive disease. Most female heterozygotes are asymptomatic; however, skewed X-inactivation has been reported in some affected females (OMIM, PMIDs: 20301357, 23689198). (I) 0115 - Variants in this gene are known to have variable expressivity. Variable expressivity of clinical findings and disease severity have been reported (PMID: 20301357). (I) 0200 - Variant is predicted to result in a missense amino acid change from isoleucine to threonine. (I) 0251 - This variant is heterozygous. (I) 0301 - Variant is absent from gnomAD (both v2 and v3). (SP) 0501 - Missense variant consistently predicted to be damaging by multiple in silico tools or highly conserved with a major amino acid change. (SP) 0600 - Variant is located in the annotated GTPase binding domain (PMID: 16804117). (I) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. It has been reported as pathogenic/likely pathogenic by multiple clinical testing laboratories (ClinVar). It has also been reported in multiple individuals with neutropenia (ClinVar, PMIDs: 35404999, 16804117). In one of those reported families, affected individuals have neutropenia, macrothrombocytopenia and renal failure, and there are three affected females who are heterozygous for this variant (PMID: 35404999). (SP) 1002 - This variant has moderate functional evidence supporting abnormal protein function. Mutant protein expressed in vitro showed an increased capacity to stimulate actin polymerisation (PMID: 16804117). (SP) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign -
Pathogenic, criteria provided, single submitter	clinical testing	Mendelics	May 28, 2019	- -
Pathogenic, criteria provided, single submitter	clinical testing	Lifecell International Pvt. Ltd	-	A Hemizygote Missense variant c.881T>C in Exon 9 of the WAS gene that results in the amino acid substitution p.Ile294Thr was identified. The observed variant has a minor allele frequency of 0% in gnomAD exomes and genomes, respectively. The severity of the impact of this variant on the protein is high, based on the effect of the protein and REVEL score. Rare Exome Variant Ensemble Learner (REVEL) is an ensembl method for predicting the pathogenicity of missense variants based on a combination of scores from 13 individual tools: MutPred, FATHMM v2.3, VEST 3.0, PolyPhen-2, SIFT, PROVEAN, MutationAssessor, MutationTaster, LRT, GERP++, SiPhy, phyloP, and phastCons. The REVEL score for an individual missense variant can range from 0 to 1, with higher scores reflecting greater likelihood that the variant is disease-causing. ClinVar has also classified this variant as Pathogenic/Likely Pathogenic (Variant ID: 29967). This variant has previously been reported for X-linked neutropenia by Beel K, et,al.,2008. Functional studies also demonstrated that the p.Ile294Thr substitution affects the normal function of the WAS protein (Beel K,et,al.,2008). Based on the above evidence this variant has been classified as Pathogenic according to the ACMG guidelines. -

not provided Pathogenic:2

Likely pathogenic, criteria provided, single submitter	clinical testing	Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen	Oct 23, 2020	- -
Pathogenic, criteria provided, single submitter	clinical testing	Genetic Services Laboratory, University of Chicago	Dec 07, 2018	DNA sequence analysis of the WAS gene demonstrated a sequence change, c.881T>C, in exon 9 that results in an amino acid change, p.Ile294Thr. This is a novel sequence change that has not previously been seen in large population databases (ExAC, gnomAD). The p.Ile294Thr change affects a highly conserved amino acid residue located in a domain of the WAS protein that is known to be functional. The p.Ile294Thr substitution appears to be deleterious using several in-silico pathogenicity prediction tools (SIFT, PolyPhen2, Align GVGD, REVEL). This sequence change has been previously described in multiple patients with congenital neutropenia (PMIDs: 19006568, 16804117). Platelet counts in affected males were all subnormal or in the low_normal range (Beel K et al., 2008). Functional studies also demonstrated that the p.Ile294Thr substitution affects the normal function of the WAS protein (PMID: 19006568). -

WAS-related disorder Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

May 30, 2023

The WAS c.881T>C variant is predicted to result in the amino acid substitution p.Ile294Thr. This variant has been reported in the hemizygous state in multiple individuals with severe congenital neutropenia (SCN) (Ancliff et al. 2006. PubMed ID: 16804117; Xia et al. 2019. PubMed ID: 31352750; Beel et al. 2008. PubMed ID: 19006568). Of note, carrier females with the variant have been reported to show a variable attenuated phenotype (Beel et al. 2008. PubMed ID: 19006568). Functional studies have shown that this variant impacts protein function (Rajmohan et al. 2009. PubMed ID: 19817875; Moulding et al. 2007. PubMed ID: 17724125). This variant has not been reported in a large population database (http://gnomad.broadinstitute.org), indicating this variant is rare. This variant is interpreted as pathogenic. -

Wiskott-Aldrich syndrome;C1839163:Thrombocytopenia 1;C1845987:X-linked severe congenital neutropenia Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Invitae

Oct 20, 2023

This sequence change replaces isoleucine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 294 of the WAS protein (p.Ile294Thr). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with neutropenia (PMID: 16804117, 19006568, 31352750). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 29967). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt WAS protein function. Experimental studies have shown that this missense change affects WAS function (PMID: 16804117, 19006568). For these reasons, this variant has been classified as Pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.98
BayesDel_addAF	Pathogenic	0.56	D
BayesDel_noAF	Pathogenic	0.56
CADD	Uncertain	25
DANN	Uncertain	1.0
DEOGEN2	Pathogenic	0.94	D
FATHMM_MKL	Uncertain	0.96	D
LIST_S2	Uncertain	0.95	D
M_CAP	Pathogenic	0.54	D
MetaRNN	Pathogenic	0.98	D
MetaSVM	Uncertain	0.74	D
MutationAssessor	Pathogenic	3.3	M
MutationTaster	Benign	1.0	D
PrimateAI	Uncertain	0.78	T
PROVEAN	Pathogenic	-4.6	D
REVEL	Pathogenic	0.92
Sift	Uncertain	0.0010	D
Sift4G	Pathogenic	0.0010	D
Polyphen		1.0	D
Vest4		0.89
MutPred		0.90		Gain of disorder (P = 0.039);
MVP		0.98
MPC		1.8
ClinPred		1.0	D
GERP RS		4.7
Varity_R		0.97
gMVP		0.96

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs387906717; hg19: chrX-48546792;