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GeneBe

rs988478105

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_021167.5(GATAD1):c.157G>A(p.Gly53Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000266 in 1,126,976 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Uncertain significancein ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G53W) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 33)
Exomes 𝑓: 0.0000027 ( 0 hom. )

Consequence

GATAD1
NM_021167.5 missense

Scores

3
3
13

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.65
Variant links:
Genes affected
GATAD1 (HGNC:29941): (GATA zinc finger domain containing 1) The protein encoded by this gene contains a zinc finger at the N-terminus, and is thought to bind to a histone modification site that regulates gene expression. Mutations in this gene have been associated with autosomal recessive dilated cardiomyopathy. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jun 2012]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.22008383).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
GATAD1NM_021167.5 linkuse as main transcriptc.157G>A p.Gly53Arg missense_variant 1/5 ENST00000287957.5

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
GATAD1ENST00000287957.5 linkuse as main transcriptc.157G>A p.Gly53Arg missense_variant 1/51 NM_021167.5 P1
GATAD1ENST00000644160.1 linkuse as main transcriptn.13G>A non_coding_transcript_exon_variant 1/2
GATAD1ENST00000645746.1 linkuse as main transcriptc.157G>A p.Gly53Arg missense_variant, NMD_transcript_variant 1/6

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
AF:
0.00000266
AC:
3
AN:
1126976
Hom.:
0
Cov.:
30
AF XY:
0.00000185
AC XY:
1
AN XY:
539856
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.000207
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
33
Bravo
AF:
0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.27
BayesDel_addAF
Pathogenic
0.17
D
BayesDel_noAF
Uncertain
0.010
Cadd
Benign
22
Dann
Benign
0.97
DEOGEN2
Benign
0.0033
T
Eigen
Benign
-0.19
Eigen_PC
Benign
-0.20
FATHMM_MKL
Benign
0.69
D
LIST_S2
Benign
0.55
T
M_CAP
Pathogenic
0.85
D
MetaRNN
Benign
0.22
T
MetaSVM
Uncertain
0.24
D
MutationAssessor
Benign
0.0
N
MutationTaster
Benign
1.0
D
PrimateAI
Pathogenic
0.90
D
PROVEAN
Benign
0.21
N
REVEL
Benign
0.28
Sift
Benign
0.073
T
Sift4G
Uncertain
0.0050
D
Polyphen
0.73
P
Vest4
0.17
MutPred
0.32
Gain of methylation at G53 (P = 0.0052);
MVP
0.39
MPC
0.36
ClinPred
0.41
T
GERP RS
4.1
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Varity_R
0.11
gMVP
0.16

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs988478105; hg19: chr7-92077200; API