NM_014795.4:c.3134A>T

Variant names:

• chr2-144389962-T-A
• rs397515449
• NM_014795.4:c.3134A>T

Variant summary

Our verdict is Pathogenic. The variant received 10 ACMG points: 10P and 0B. PM1 PM2 PM5 PP3_Moderate PP5_Moderate

The NM_014795.4(ZEB2):​c.3134A>T​(p.His1045Leu) 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. 13/22 in silico tools predict a damaging 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. H1045R) has been classified as Pathogenic.

• Frequency: Genomes: not found (cov: 32)
• Consequence: ZEB2 NM_014795.4 missense
• Clinical Significance: Pathogenic criteria provided, single submitter P:1
• Conservation: PhyloP100: 8.02
• Publications: 0 publications found

Genes affected

ZEB2 (HGNC:14881): (zinc finger E-box binding homeobox 2) The protein encoded by this gene is a member of the Zfh1 family of 2-handed zinc finger/homeodomain proteins. It is located in the nucleus and functions as a DNA-binding transcriptional repressor that interacts with activated SMADs. Mutations in this gene are associated with Hirschsprung disease/Mowat-Wilson syndrome. Alternatively spliced transcript variants have been found for this gene.[provided by RefSeq, Jan 2010]

ZEB2 Gene-Disease associations (from GenCC):

• Mowat-Wilson syndrome

  Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Ambry Genetics, ClinGen, Labcorp Genetics (formerly Invitae), G2P

ACMG classification

Our verdict: Pathogenic. The variant received 10 ACMG points.

• PM1: In a hotspot region, there are 5 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 0 benign, 7 uncertain in NM_014795.4
• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr2-144389962-T-C is described in CliVar as Pathogenic. Clinvar id is 56827.Status of the report is no_assertion_criteria_provided, 0 stars.
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.897
• PP5: Variant 2-144389962-T-A is Pathogenic according to our data. Variant chr2-144389962-T-A is described in CliVar as Pathogenic. Clinvar id is 2837185.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr2-144389962-T-A is described in CliVar as Pathogenic. Clinvar id is 2837185.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr2-144389962-T-A is described in CliVar as Pathogenic. Clinvar id is 2837185.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr2-144389962-T-A is described in CliVar as Pathogenic. Clinvar id is 2837185.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr2-144389962-T-A is described in CliVar as Pathogenic. Clinvar id is 2837185.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr2-144389962-T-A is described in CliVar as Pathogenic. Clinvar id is 2837185.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr2-144389962-T-A is described in CliVar as Pathogenic. Clinvar id is 2837185.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr2-144389962-T-A is described in CliVar as Pathogenic. Clinvar id is 2837185.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr2-144389962-T-A is described in CliVar as Pathogenic. Clinvar id is 2837185.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr2-144389962-T-A is described in CliVar as Pathogenic. Clinvar id is 2837185.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr2-144389962-T-A is described in CliVar as Pathogenic. Clinvar id is 2837185.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr2-144389962-T-A is described in CliVar as Pathogenic. Clinvar id is 2837185.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr2-144389962-T-A is described in CliVar as Pathogenic. Clinvar id is 2837185.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr2-144389962-T-A is described in CliVar as Pathogenic. Clinvar id is 2837185.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr2-144389962-T-A is described in CliVar as Pathogenic. Clinvar id is 2837185.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr2-144389962-T-A is described in CliVar as Pathogenic. Clinvar id is 2837185.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr2-144389962-T-A is described in CliVar as Pathogenic. Clinvar id is 2837185.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr2-144389962-T-A is described in CliVar as Pathogenic. Clinvar id is 2837185.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr2-144389962-T-A is described in CliVar as Pathogenic. Clinvar id is 2837185.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr2-144389962-T-A is described in CliVar as Pathogenic. Clinvar id is 2837185.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr2-144389962-T-A is described in CliVar as Pathogenic. Clinvar id is 2837185.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr2-144389962-T-A is described in CliVar as Pathogenic. Clinvar id is 2837185.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr2-144389962-T-A is described in CliVar as Pathogenic. Clinvar id is 2837185.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr2-144389962-T-A is described in CliVar as Pathogenic. Clinvar id is 2837185.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr2-144389962-T-A is described in CliVar as Pathogenic. Clinvar id is 2837185.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZEB2	NM_014795.4	c.3134A>T	p.His1045Leu	missense_variant	Exon 10 of 10	ENST00000627532.3	NP_055610.1
ZEB2	NM_001171653.2	c.3062A>T	p.His1021Leu	missense_variant	Exon 9 of 9		NP_001165124.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZEB2	ENST00000627532.3	c.3134A>T	p.His1045Leu	missense_variant	Exon 10 of 10	1	NM_014795.4	ENSP00000487174.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: criteria provided, single submitter

Submissions by phenotype

Mowat-Wilson syndrome Pathogenic:1

Mar 15, 2023

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

For these reasons, this variant has been classified as Pathogenic. This variant disrupts the p.His1045 amino acid residue in ZEB2. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 23466526). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. 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 ZEB2 protein function. This missense change has been observed in individual(s) with clinical features of Mowat-Wilson syndrome (Invitae). In at least one individual the variant was observed to be de novo. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces histidine, which is basic and polar, with leucine, which is neutral and non-polar, at codon 1045 of the ZEB2 protein (p.His1045Leu). -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	1.0
BayesDel_addAF	Pathogenic	0.47	D
BayesDel_noAF	Pathogenic	0.44
CADD	Pathogenic	33
DANN	Uncertain	0.98
DEOGEN2	Uncertain	0.44	T;T;T;T;T;.;T;D;D;T;.;D;D
Eigen	Pathogenic	1.0
Eigen_PC	Pathogenic	0.88
FATHMM_MKL	Pathogenic	0.97	D
LIST_S2	Benign	0.84	.;.;.;.;T;T;T;.;.;T;T;T;T
M_CAP	Pathogenic	0.70	D
MetaRNN	Pathogenic	0.90	D;D;D;D;D;D;D;D;D;D;D;D;D
MetaSVM	Pathogenic	1.0	D
MutationAssessor	Pathogenic	3.9	.;.;.;.;.;.;.;H;H;.;.;H;.
PhyloP100		8.0
PrimateAI	Pathogenic	0.92	D
PROVEAN	Pathogenic	-9.8	.;.;.;.;.;.;.;.;D;.;D;D;.
REVEL	Pathogenic	0.82
Sift	Pathogenic	0.0	.;.;.;.;.;.;.;.;D;.;D;D;.
Sift4G	Pathogenic	0.0	.;.;.;.;.;.;.;D;D;.;D;D;D
Polyphen		1.0	.;.;.;.;.;.;.;D;D;.;.;D;D
Vest4		0.91, 0.94, 0.96, 0.93, 0.95
MutPred		0.41		.;.;.;.;.;.;.;Loss of catalytic residue at I1043 (P = 0.0923);Loss of catalytic residue at I1043 (P = 0.0923);Loss of catalytic residue at I1043 (P = 0.0923);.;Loss of catalytic residue at I1043 (P = 0.0923);.;
MVP		0.92
MPC		1.8
ClinPred		1.0	D
GERP RS		5.6
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.93
gMVP		1.0
Mutation Taster		=5/95	disease causing

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

Other links and lift over

dbSNP: rs397515449; hg19: chr2-145147529;