Variant chrX-46985745-T-C details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_014735.5(JADE3):c.79T>C(p.Tyr27His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000892 in 112,048 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. In-silico tool predicts a benign outcome for this variant. 11/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.0000089 ( 0 hom., 0 hem., cov: 22)

Consequence

JADE3
NM_014735.5 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 3.05

Variant links:

Genes affected

JADE3 (HGNC:22982): (jade family PHD finger 3) This gene encodes a member of a family of large proteins containing PHD (plant homeo domain)-type zinc fingers. The encoded protein may be associated in a nuclear complex that functions in histone H4 acetylation. Alternative splicing results in multiple transcript variants encoding the same protein. [provided by RefSeq, Aug 2013]

JADE3 links:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.15097794).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
JADE3	NM_014735.5 linkuse as main transcript	c.79T>C	p.Tyr27His	missense_variant	3/11	ENST00000614628.5	NP_055550.1	Q92613A0A024R1A2
JADE3	NM_001077445.3 linkuse as main transcript	c.79T>C	p.Tyr27His	missense_variant	3/11		NP_001070913.1	Q92613A0A024R1A2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
JADE3	ENST00000614628.5 linkuse as main transcript	c.79T>C	p.Tyr27His	missense_variant	3/11	1	NM_014735.5	ENSP00000481850.1	Q92613
JADE3	ENST00000611250.4 linkuse as main transcript	c.79T>C	p.Tyr27His	missense_variant	3/11	2		ENSP00000479377.1	Q92613
JADE3	ENST00000424392.5 linkuse as main transcript	c.79T>C	p.Tyr27His	missense_variant	3/6	3		ENSP00000391009.1	F2Z3N8
JADE3	ENST00000455411.1 linkuse as main transcript	c.79T>C	p.Tyr27His	missense_variant	3/5	4		ENSP00000400584.1	F2Z2B6

Frequencies

GnomAD3 genomes

AF:

0.00000892

AC:

AN:

112048

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

34204

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000188

Gnomad OTH

AF:

0.00

GnomAD4 exome

Cov.:

GnomAD4 genome

AF:

0.00000892

AC:

AN:

112048

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

34204

show subpopulations

Gnomad4 AFR

AF:

0.00

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000188

Gnomad4 OTH

AF:

0.00

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

May 18, 2022

The c.79T>C (p.Y27H) alteration is located in exon 3 (coding exon 2) of the JADE3 gene. This alteration results from a T to C substitution at nucleotide position 79, causing the tyrosine (Y) at amino acid position 27 to be replaced by a histidine (H). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.14

BayesDel_addAF

Uncertain

0.041

BayesDel_noAF

Benign

-0.18

CADD

Benign

DANN

Uncertain

0.99

DEOGEN2

Benign

0.057

.;T;T;T

FATHMM_MKL

Uncertain

0.82

LIST_S2

Benign

0.54

T;T;.;T

M_CAP

Benign

0.0044

MetaRNN

Benign

0.15

T;T;T;T

MetaSVM

Benign

-1.0

MutationAssessor

Benign

1.4

.;L;L;.

PrimateAI

Uncertain

0.63

PROVEAN

Benign

0.50

N;.;.;N

REVEL

Benign

0.18

Sift

Benign

0.36

T;.;.;T

Sift4G

Benign

0.54

T;T;T;T

Polyphen

1.0

.;D;D;.

Vest4

0.32, 0.36

MutPred

0.17

Loss of phosphorylation at Y27 (P = 0.031);Loss of phosphorylation at Y27 (P = 0.031);Loss of phosphorylation at Y27 (P = 0.031);Loss of phosphorylation at Y27 (P = 0.031);

MVP

0.61

ClinPred

0.59

GERP RS

4.7

Varity_R

0.10

gMVP

0.52

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over