X-69957097-G-T

Position:

• chrX-69957097-G-T

Variant summary

Our verdict is Likely pathogenic. Variant got 9 ACMG points: 9P and 0B. PM1 PM2 PM5 PP3 PP5_Moderate

The NM_001399.5(EDA):​c.467G>T​(p.Arg156Leu) variant causes a missense change. 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 Pathogenic (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R156C) has been classified as Likely pathogenic.

• Frequency: Genomes: not found (cov: 23)
• Consequence: EDA NM_001399.5 missense
• Clinical Significance: Pathogenic criteria provided, single submitter P:1
• Conservation: PhyloP100: 5.55

Genes affected

EDA (HGNC:3157): (ectodysplasin A) The protein encoded by this gene is a type II membrane protein that can be cleaved by furin to produce a secreted form. The encoded protein, which belongs to the tumor necrosis factor family, acts as a homotrimer and may be involved in cell-cell signaling during the development of ectodermal organs. Defects in this gene are a cause of ectodermal dysplasia, anhidrotic, which is also known as X-linked hypohidrotic ectodermal dysplasia. Several transcript variants encoding many different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Likely_pathogenic. Variant got 9 ACMG points.

• PM1: In a region_of_interest Disordered (size 99) in uniprot entity EDA_HUMAN there are 53 pathogenic changes around while only 7 benign (88%) in NM_001399.5
• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chrX-69957096-C-T is described in ClinVar as [Likely_pathogenic]. Clinvar id is 11036.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.805
• PP5: Variant X-69957097-G-T is Pathogenic according to our data. Variant chrX-69957097-G-T is described in ClinVar as [Pathogenic]. Clinvar id is 44194.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chrX-69957097-G-T is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EDA	NM_001399.5	c.467G>T	p.Arg156Leu	missense_variant	2/8	ENST00000374552.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EDA	ENST00000374552.9	c.467G>T	p.Arg156Leu	missense_variant	2/8	1	NM_001399.5	P4

Frequencies

GnomAD3 genomes Cov.: 23

GnomAD4 exome Cov.: 29

GnomAD4 genome Cov.: 23

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: criteria provided, single submitter

Submissions by phenotype

Hypohidrotic X-linked ectodermal dysplasia Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 03, 2015

The p.Arg156Leu variant in EDA has been reported in 1 adult male with X-linked h ypohidrotic ectodermal dysplasia (XLHED; Dietz 2013), and was absent from large population studies. In addition, several variants affecting the same amino acid position (p.Arg156His, p.Arg156Cys, p.Arg156Gly, p.Arg156Ser) have been identifi ed in multiple individuals with X-linked hypohidrotic ectodermal dysplasia and s egregated with disease in those families, suggesting that the arginine (Arg) res idue at position 156 is intolerant to variation (Monreal 1998, Aoki 2000, Schnei der 2001, Vincent 2001, Schneider 2011, Zhao 2008, Cluzeau 2011, Clauss 2010, Li 2013, He 2013, Dietz 2013). In vitro functional studies provide evidence that a change affecting this amino acid position disrupts the normal processing and fu nction of the EDA protein (Chen 2001), consistent with a causal role for variant s identified at this position. In summary, this variant meets our criteria to be classified as pathogenic for X-linked hypohidrotic ectodermal dysplasia (http:/ /www.partners.org/personalizedmedicine/LMM) based upon the presence of this vari ant as well as other variants affecting the same position in several affected in dividuals, and the functional evidence. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.87
BayesDel_addAF	Pathogenic	0.18	D
BayesDel_noAF	Uncertain	0.020
CADD	Uncertain	24
DANN	Uncertain	1.0
DEOGEN2	Uncertain	0.45	.;T;.;.;.
FATHMM_MKL	Uncertain	0.92	D
LIST_S2	Uncertain	0.93	D;D;D;D;D
M_CAP	Pathogenic	0.53	D
MetaRNN	Pathogenic	0.81	D;D;D;D;D
MetaSVM	Uncertain	0.41	D
MutationAssessor	Benign	0.90	L;L;L;.;.
MutationTaster	Benign	0.98	D;D;D
PrimateAI	Uncertain	0.54	T
PROVEAN	Benign	-1.8	N;N;N;N;.
REVEL	Uncertain	0.52
Sift	Uncertain	0.016	D;.;.;D;.
Sift4G	Benign	0.30	T;T;T;T;D
Polyphen		0.94	P;P;D;.;.
Vest4		0.67
MutPred		0.69		Loss of MoRF binding (P = 0.0449);Loss of MoRF binding (P = 0.0449);Loss of MoRF binding (P = 0.0449);.;.;
MVP		0.98
MPC		0.97
ClinPred		0.81	D
GERP RS		5.0
Varity_R		0.77
gMVP		0.94

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs132630314; hg19: chrX-69176947;