chr1-153810179-A-G

Position:

• chr1-153810179-A-G

Variant summary

Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2 PM4 PP5_Moderate

The NM_020699.4(GATAD2B):​c.1780T>C​(p.Ter594GlnextTer91) variant causes a stop lost change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: GATAD2B NM_020699.4 stop_lost
• Clinical Significance: Likely pathogenic criteria provided, single submitter P:1
• Conservation: PhyloP100: 7.09

Genes affected

GATAD2B (HGNC:30778): (GATA zinc finger domain containing 2B) This gene encodes a zinc finger protein transcriptional repressor. The encoded protein is part of the methyl-CpG-binding protein-1 complex, which represses gene expression by deacetylating methylated nucleosomes. Mutations in this gene are linked to intellectual disability and dysmorphic features associated with cognitive disability. [provided by RefSeq, Jun 2016]

ACMG classification

Verdict is Likely_pathogenic. Variant got 6 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PM4: Stoplost variant in NM_020699.4 Downstream stopcodon found after 6 codons.
• PP5: Variant 1-153810179-A-G is Pathogenic according to our data. Variant chr1-153810179-A-G is described in ClinVar as [Likely_pathogenic]. Clinvar id is 1029765.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GATAD2B	NM_020699.4	c.1780T>C	p.Ter594GlnextTer91	stop_lost	11/11	ENST00000368655.5	NP_065750.1
GATAD2B	XM_047426115.1	c.1783T>C	p.Ter595GlnextTer91	stop_lost	11/11		XP_047282071.1
GATAD2B	XM_047426117.1	c.1780T>C	p.Ter594GlnextTer91	stop_lost	11/11		XP_047282073.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GATAD2B	ENST00000368655.5	c.1780T>C	p.Ter594GlnextTer91	stop_lost	11/11	1	NM_020699.4	ENSP00000357644	P1
GATAD2B	ENST00000634544.1	c.1780T>C	p.Ter594GlnextTer91	stop_lost	11/11	5		ENSP00000489184	P1
GATAD2B	ENST00000634408.1	c.1732T>C	p.Ter578GlnextTer?	stop_lost	11/11	5		ENSP00000489595
GATAD2B	ENST00000637918.1	c.135+1552T>C		intron_variant		5		ENSP00000490724

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 32

ClinVar

Significance: Likely pathogenic

Submissions summary: Pathogenic:1

Revision: criteria provided, single submitter

Submissions by phenotype

Severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Baylor Genetics

Apr 18, 2019

This variant was determined to be likely pathogenic according to ACMG Guidelines, 2015 [PMID:25741868]. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Benign	-0.035	T
BayesDel_noAF	Benign	-0.29
CADD	Benign	18
DANN	Benign	0.91
Eigen	Pathogenic	1.1
Eigen_PC	Pathogenic	0.97
FATHMM_MKL	Pathogenic	1.0	D
MutationTaster	Benign	1.0	N
Vest4		0.090
GERP RS		5.4
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7

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: rs1674245097; hg19: chr1-153782655;