NM_014795.4:c.2329C>A

Variant names:

• chr2-144398858-G-T
• rs587784564
• NM_014795.4:c.2329C>A

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2 BP4

The NM_014795.4(ZEB2):​c.2329C>A​(p.His777Asn) 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 benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: ZEB2 NM_014795.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 9.92

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.29222387).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZEB2	NM_014795.4	c.2329C>A	p.His777Asn	missense_variant	Exon 8 of 10	ENST00000627532.3	NP_055610.1
ZEB2	NM_001171653.2	c.2257C>A	p.His753Asn	missense_variant	Exon 7 of 9		NP_001165124.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZEB2	ENST00000627532.3	c.2329C>A	p.His777Asn	missense_variant	Exon 8 of 10	1	NM_014795.4	ENSP00000487174.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.20
BayesDel_addAF	Benign	-0.078	T
BayesDel_noAF	Benign	-0.35
CADD	Uncertain	25
DANN	Uncertain	0.98
DEOGEN2	Benign	0.014	T;T;T;T;T;.;T;T;T;T;.;T;T
Eigen	Pathogenic	0.70
Eigen_PC	Pathogenic	0.74
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Uncertain	0.93	.;.;.;.;D;D;D;.;.;D;D;D;D
M_CAP	Benign	0.0090	T
MetaRNN	Benign	0.29	T;T;T;T;T;T;T;T;T;T;T;T;T
MetaSVM	Benign	-1.2	T
MutationAssessor	Benign	1.1	.;.;.;.;.;.;.;L;L;.;.;L;.
PrimateAI	Uncertain	0.70	T
PROVEAN	Benign	-0.81	.;.;.;.;.;.;.;.;N;.;N;N;.
REVEL	Benign	0.27
Sift	Benign	0.20	.;.;.;.;.;.;.;.;T;.;T;T;.
Sift4G	Benign	0.54	.;.;.;.;.;.;.;T;T;.;T;T;T
Polyphen		0.96	.;.;.;.;.;.;.;D;D;.;.;D;D
Vest4		0.84, 0.74, 0.83, 0.75, 0.79
MutPred		0.11		.;.;.;.;.;.;.;Gain of methylation at K774 (P = 0.1618);Gain of methylation at K774 (P = 0.1618);Gain of methylation at K774 (P = 0.1618);.;Gain of methylation at K774 (P = 0.1618);.;
MVP		0.29
MPC		1.4
ClinPred		0.61	D
GERP RS		5.4
Varity_R		0.15
gMVP		0.31

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: rs587784564; hg19: chr2-145156425;