2-144404846-T-G

Variant names:

• chr2-144404846-T-G
• rs918109625
• NM_014795.4:c.582A>C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Moderate BP6_Moderate

The NM_014795.4(ZEB2):​c.582A>C​(p.Gln194His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 16/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Synonymous variant affecting the same amino acid position (i.e. Q194Q) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: ZEB2 NM_014795.4 missense
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.413
• 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.08758542).
• BP6: Variant 2-144404846-T-G is Benign according to our data. Variant chr2-144404846-T-G is described in ClinVar as Benign. ClinVar VariationId is 1660286.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.582A>C	p.Gln194His	missense_variant	Exon 5 of 10	ENST00000627532.3	NP_055610.1
ZEB2	NM_001171653.2	c.510A>C	p.Gln170His	missense_variant	Exon 4 of 9		NP_001165124.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZEB2	ENST00000627532.3	c.582A>C	p.Gln194His	missense_variant	Exon 5 of 10	1	NM_014795.4	ENSP00000487174.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Mowat-Wilson syndrome Benign:1

Jan 02, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.13
BayesDel_addAF	Benign	-0.080	T
BayesDel_noAF	Benign	-0.35
CADD	Benign	19
DANN	Benign	0.80
DEOGEN2	Benign	0.0079	T;T;T;T;T;T;T;T;T;.;T;T;T;T;.;T;.
Eigen	Benign	-0.64
Eigen_PC	Benign	-0.41
FATHMM_MKL	Benign	0.69	D
LIST_S2	Benign	0.78	.;.;.;.;T;D;.;.;T;D;T;T;T;T;T;T;T
M_CAP	Benign	0.011	T
MetaRNN	Benign	0.088	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T
MetaSVM	Benign	-0.97	T
MutationAssessor	Benign	-0.17	.;.;.;.;.;.;N;N;.;.;N;.;.;.;.;.;.
PhyloP100		0.41
PrimateAI	Uncertain	0.73	T
PROVEAN	Benign	0.44	.;.;.;.;.;.;.;N;.;N;N;.;.;.;.;.;.
REVEL	Benign	0.20
Sift	Benign	1.0	.;.;.;.;.;.;.;T;.;T;T;.;.;.;.;.;.
Sift4G	Benign	0.97	.;.;.;.;.;.;T;T;.;T;T;T;T;.;.;T;.
Polyphen		0.0	.;.;.;.;.;.;B;B;.;.;B;B;.;.;.;.;.
Vest4		0.35, 0.35, 0.27, 0.31, 0.35, 0.34
MutPred		0.22		.;.;.;.;.;Loss of loop (P = 0.1258);Loss of loop (P = 0.1258);Loss of loop (P = 0.1258);Loss of loop (P = 0.1258);.;Loss of loop (P = 0.1258);.;.;.;Loss of loop (P = 0.1258);.;.;
MVP		0.41
MPC		0.66
ClinPred		0.11	T
GERP RS		3.3
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.8
Varity_R		0.034
gMVP		0.55
Mutation Taster		=70/30	polymorphism

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: rs918109625; hg19: chr2-145162413;