Genetic Variant UXT:p.Gln29Lys (chrX-47658843-G-T) – ACMG Classification: Likely_benign (-5 pts)

Variant summary

Our verdict is Likely benign. The variant received -5 ACMG points: 0P and 5B. BP4BS2

The NM_004182.4(UXT):c.85C>A(p.Gln29Lys) variant causes a missense change. The variant allele was found at a frequency of 0.0000288 in 1,145,575 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 7 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.00019 ( 0 hom., 5 hem., cov: 24)

Exomes 𝑓: 0.000012 ( 0 hom. 2 hem. )

Consequence

UXT
NM_004182.4 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 4.40

Publications

0 publications found

Variant links:

Genes affected

UXT (HGNC:12641): (ubiquitously expressed prefoldin like chaperone) The protein encoded by this gene functions as a cofactor that modulates androgen receptor-dependent transcription, and also plays a critical role in tumor necrosis factor-induced apoptosis. Expression of this gene may play a role in tumorigenesis. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Nov 2011]

UXT links:

UXT-AS1 (HGNC:49239): (UXT antisense RNA 1)

UXT-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -5 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.3516975).

BS2

High Hemizygotes in GnomAd4 at 5 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004182.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
UXT	NM_004182.4	MANE Select	c.85C>A	p.Gln29Lys	missense	Exon 2 of 7	NP_004173.1	Q9UBK9-1
UXT	NM_153477.3		c.121C>A	p.Gln41Lys	missense	Exon 1 of 6	NP_705582.1	Q9UBK9-2
UXT-AS1	NR_028119.1		n.11G>T		non_coding_transcript_exon	Exon 1 of 2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
UXT	ENST00000333119.8	TSL:1 MANE Select	c.85C>A	p.Gln29Lys	missense	Exon 2 of 7	ENSP00000327797.3	Q9UBK9-1
UXT	ENST00000335890.3	TSL:1	c.121C>A	p.Gln41Lys	missense	Exon 1 of 6	ENSP00000337393.2	Q9UBK9-2
UXT	ENST00000936479.1		c.85C>A	p.Gln29Lys	missense	Exon 2 of 7	ENSP00000606538.1

Frequencies

GnomAD3 genomes

AF:

0.000186

AC:

AN:

112968

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000610

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0000929

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

GnomAD2 exomes

AF:

0.0000466

AC:

AN:

128668

AF XY:

0.0000253

show subpopulations

Gnomad AFR exome

AF:

0.000500

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.0000116

AC:

AN:

1032607

Hom.:

Cov.:

AF XY:

0.00000606

AC XY:

AN XY:

330239

show subpopulations

African (AFR)

AF:

0.000414

AC:

AN:

24133

American (AMR)

AF:

0.0000808

AC:

AN:

24750

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

15076

East Asian (EAS)

AF:

0.00

AC:

AN:

29249

South Asian (SAS)

AF:

0.00

AC:

AN:

44651

European-Finnish (FIN)

AF:

0.00

AC:

AN:

37988

Middle Eastern (MID)

AF:

0.00

AC:

AN:

3826

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

809791

Other (OTH)

AF:

0.00

AC:

AN:

43143

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.000186

AC:

AN:

112968

Hom.:

Cov.:

AF XY:

0.000142

AC XY:

AN XY:

35098

show subpopulations

African (AFR)

AF:

0.000610

AC:

AN:

31129

American (AMR)

AF:

0.0000929

AC:

AN:

10767

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

2662

East Asian (EAS)

AF:

0.00

AC:

AN:

3594

South Asian (SAS)

AF:

0.00

AC:

AN:

2796

European-Finnish (FIN)

AF:

0.00

AC:

AN:

6243

Middle Eastern (MID)

AF:

0.00

AC:

AN:

239

European-Non Finnish (NFE)

AF:

0.0000188

AC:

AN:

53333

Other (OTH)

AF:

0.00

AC:

AN:

1520

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.487

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.000142

Hom.:

Bravo

AF:

0.000246

ESP6500AA

AF:

0.000522

AC:

ESP6500EA

AF:

0.00

AC:

ExAC

AF:

0.0000676

AC:

ClinVar

ClinVar submissions

Significance:Uncertain significance

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not specified (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.14

BayesDel_addAF

Benign

-0.28

BayesDel_noAF

Benign

-0.25

CADD

Benign

(source)

DANN

Benign

0.90

DEOGEN2

Benign

0.14

FATHMM_MKL

Uncertain

0.77

LIST_S2

Benign

0.83

M_CAP

Pathogenic

0.34

MetaRNN

Benign

0.35

MetaSVM

Benign

-0.63

MutationAssessor

Benign

0.13

PhyloP100

4.4

PrimateAI

Uncertain

0.52

PROVEAN

Benign

0.40

REVEL

Uncertain

0.34

Sift

Benign

1.0

Sift4G

Benign

0.92

Polyphen

0.0010

Vest4

0.52

MVP

0.83

MPC

0.70

ClinPred

0.072

GERP RS

5.3

PromoterAI

0.046

Neutral

(source)

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Varity_R

0.38

gMVP

0.54

Mutation Taster

=96/4

polymorphism

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over