2-144396547-C-A

Position:

• chr2-144396547-C-A

Variant summary

Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM2 PP2 PP5_Moderate

The NM_014795.4(ZEB2):​c.2932G>T​(p.Asp978Tyr) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Likely pathogenic (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: ZEB2 NM_014795.4 missense
• Clinical Significance: Likely pathogenic criteria provided, single submitter P:1
• Conservation: PhyloP100: 5.95

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 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 5 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP2: Missense variant in gene, where missense usually causes diseases (based on misZ statistic), ZEB2. . Gene score misZ 3.9433 (greater than the threshold 3.09). Trascript score misZ 5.6227 (greater than threshold 3.09). GenCC has associacion of gene with Mowat-Wilson syndrome.
• PP5: Variant 2-144396547-C-A is Pathogenic according to our data. Variant chr2-144396547-C-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 217029.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZEB2	NM_014795.4	c.2932G>T	p.Asp978Tyr	missense_variant	9/10	ENST00000627532.3	NP_055610.1
ZEB2	NM_001171653.2	c.2860G>T	p.Asp954Tyr	missense_variant	8/9		NP_001165124.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZEB2	ENST00000627532.3	c.2932G>T	p.Asp978Tyr	missense_variant	9/10	1	NM_014795.4	ENSP00000487174.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

ClinVar

Significance: Likely pathogenic

Submissions summary: Pathogenic:1

Revision: criteria provided, single submitter

Submissions by phenotype

Mowat-Wilson syndrome Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

UCLA Clinical Genomics Center, UCLA

Jul 17, 2012

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.75
BayesDel_addAF	Pathogenic	0.22	D
BayesDel_noAF	Uncertain	0.080
CADD	Pathogenic	30
DANN	Uncertain	1.0
DEOGEN2	Benign	0.12	.;T;T;T;T;T;.;T;D;D;T;.;.;D;T
Eigen	Uncertain	0.55
Eigen_PC	Uncertain	0.63
FATHMM_MKL	Uncertain	0.97	D
LIST_S2	Uncertain	0.97	D;.;.;.;.;D;D;D;.;.;D;D;D;D;D
M_CAP	Benign	0.021	T
MetaRNN	Uncertain	0.61	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D
MetaSVM	Benign	-1.1	T
MutationAssessor	Uncertain	2.2	.;.;.;.;.;.;.;.;M;M;.;.;.;M;.
PrimateAI	Pathogenic	0.89	D
PROVEAN	Uncertain	-4.3	.;.;.;.;.;.;.;.;.;D;.;.;D;D;D
REVEL	Benign	0.28
Sift	Pathogenic	0.0	.;.;.;.;.;.;.;.;.;D;.;.;D;D;D
Sift4G	Uncertain	0.0080	.;.;.;.;.;.;.;.;D;D;.;.;D;D;D
Polyphen		0.59	.;.;.;.;.;.;.;.;P;P;.;.;.;P;P
Vest4		0.92, 0.87, 0.92, 0.94, 0.91
MutPred		0.32		.;.;.;.;.;.;.;.;Gain of phosphorylation at D978 (P = 0.0262);Gain of phosphorylation at D978 (P = 0.0262);Gain of phosphorylation at D978 (P = 0.0262);.;.;Gain of phosphorylation at D978 (P = 0.0262);.;
MVP		0.45
MPC		2.8
ClinPred		1.0	D
GERP RS		5.9
Varity_R		0.78
gMVP		0.82

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: rs863224942; hg19: chr2-145154114;