X-9653599-G-C

Variant names:

• chrX-9653599-G-C
• rs138597617
• NM_005647.4:c.13G>C

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

The NM_005647.4(TBL1X):​c.13G>C​(p.Ala5Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000342 in 1,168,593 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 2 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A5T) has been classified as Uncertain significance.

• Frequency:
  • Genomes: 𝑓 0.0000089 (0 hom., 0 hem., cov: 23)
  • Exomes 𝑓: 0.0000028 (0 hom. 2 hem.)
• Consequence: TBL1X NM_005647.4 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: -3.57
• Publications: 1 publications found

Genes affected

TBL1X (HGNC:11585): (transducin beta like 1 X-linked) The protein encoded by this gene has sequence similarity with members of the WD40 repeat-containing protein family. The WD40 group is a large family of proteins, which appear to have a regulatory function. It is believed that the WD40 repeats mediate protein-protein interactions and members of the family are involved in signal transduction, RNA processing, gene regulation, vesicular trafficking, cytoskeletal assembly and may play a role in the control of cytotypic differentiation. This encoded protein is found as a subunit in corepressor SMRT (silencing mediator for retinoid and thyroid receptors) complex along with histone deacetylase 3 protein. This gene is located adjacent to the ocular albinism gene and it is thought to be involved in the pathogenesis of the ocular albinism with late-onset sensorineural deafness phenotype. Four transcript variants encoding two different isoforms have been found for this gene. This gene is highly similar to the Y chromosome TBL1Y gene. [provided by RefSeq, Nov 2008]

TBL1X Gene-Disease associations (from GenCC):

• hypothyroidism, congenital, nongoitrous, 8

  Inheritance: Unknown, XL Classification: STRONG, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, PanelApp Australia

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.0658142).
• BS2: High Hemizygotes in GnomAdExome4 at 2 XL,Unknown gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005647.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TBL1X	NM_005647.4	MANE Select	c.13G>C	p.Ala5Pro	missense	Exon 4 of 18	NP_005638.1	O60907-1
	TBL1X	NM_001139466.1		c.13G>C	p.Ala5Pro	missense	Exon 4 of 18	NP_001132938.1	O60907-1
	TBL1X	NM_001139467.1		c.-50-616G>C		intron	N/A	NP_001132939.1	O60907-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TBL1X	ENST00000645353.2	MANE Select	c.13G>C	p.Ala5Pro	missense	Exon 4 of 18	ENSP00000496215.1	O60907-1
	TBL1X	ENST00000380961.5	TSL:1	c.-50-616G>C		intron	N/A	ENSP00000370348.1	O60907-2
	TBL1X	ENST00000407597.7	TSL:2	c.13G>C	p.Ala5Pro	missense	Exon 4 of 18	ENSP00000385988.2	O60907-1

Frequencies

GnomAD3 genomes AF: 0.00000887 AC: 1 AN: 112687 Hom.: 0 Cov.: 23

Gnomad AFR AF: 0.0000322

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: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.00000284 AC: 3 AN: 1055906 Hom.: 0 Cov.: 30 AF XY: 0.00000580 AC XY: 2 AN XY: 344986

African (AFR) AF: 0.0000800 AC: 2 AN: 25010

American (AMR) AF: 0.0000352 AC: 1 AN: 28398

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 18623

East Asian (EAS) AF: 0.00 AC: 0 AN: 27239

South Asian (SAS) AF: 0.00 AC: 0 AN: 49893

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 37658

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4094

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 820506

Other (OTH) AF: 0.00 AC: 0 AN: 44485

GnomAD4 genome AF: 0.00000887 AC: 1 AN: 112687 Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0 AN XY: 34851

African (AFR) AF: 0.0000322 AC: 1 AN: 31020

American (AMR) AF: 0.00 AC: 0 AN: 10707

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2650

East Asian (EAS) AF: 0.00 AC: 0 AN: 3584

South Asian (SAS) AF: 0.00 AC: 0 AN: 2760

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 6210

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 240

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 53312

Other (OTH) AF: 0.00 AC: 0 AN: 1517

Alfa AF: 0.00 Hom.: 7

Bravo AF: 0.0000189

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	Inborn genetic diseases (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.079
BayesDel_addAF	Benign	-0.23	T
BayesDel_noAF	Benign	-0.57
CADD	Benign	0.066
DANN	Benign	0.91
DEOGEN2	Benign	0.19	T
FATHMM_MKL	Benign	0.0023	N
LIST_S2	Benign	0.51	T
M_CAP	Benign	0.0086	T
MetaRNN	Benign	0.066	T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	0.0	N
PhyloP100		-3.6
PrimateAI	Benign	0.26	T
PROVEAN	Benign	0.35	N
REVEL	Benign	0.18
Sift	Uncertain	0.026	D
Sift4G	Uncertain	0.046	D
Polyphen		0.063	B
Vest4		0.15
MutPred		0.16		Gain of loop (P = 0.0435)
MVP		0.78
MPC		0.93
ClinPred		0.093	T
GERP RS		-2.6
Varity_R		0.081
gMVP		0.25
Mutation Taster		=86/14	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs138597617; hg19: chrX-9621639;