X-123613430-T-C

Variant names:

• chrX-123613430-T-C
• rs1603229932
• NM_001081550.2:c.4646A>G

Variant summary

Our verdict is Uncertain significance. The variant received 1 ACMG points: 3P and 2B. PM2 PP2 BP4_Moderate

The NM_001081550.2(THOC2):​c.4646A>G​(p.Lys1549Arg) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (no stars).

• Frequency: Genomes: not found (cov: 22)
• Consequence: THOC2 NM_001081550.2 missense
• Clinical Significance: Uncertain significance no assertion criteria provided U:1
• Conservation: PhyloP100: 3.66
• Publications: 1 publications found

Genes affected

THOC2 (HGNC:19073): (THO complex subunit 2) The TREX multiprotein complex binds specifically to spliced mRNAs to facilitate mRNA export. The protein encoded by this gene is a member of the THO complex, a subset of the TREX complex. The encoded protein interacts with the THOC1 protein.[provided by RefSeq, Jun 2010]

THOC2 Gene-Disease associations (from GenCC):

• X-linked intellectual disability-short stature-overweight syndrome

  Inheritance: XL Classification: STRONG, MODERATE, SUPPORTIVE Submitted by: G2P, Labcorp Genetics (formerly Invitae), Orphanet, Ambry Genetics

ACMG classification

Our verdict: Uncertain_significance. The variant received 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP2: Missense variant in the gene, where a lot of missense mutations are associated with disease in ClinVar. The gene has 15 curated pathogenic missense variants (we use a threshold of 10). The gene has 3 curated benign missense variants. Gene score misZ: 5.5258 (above the threshold of 3.09). Trascript score misZ: NaN (below the threshold of 3.09). GenCC associations: The gene is linked to X-linked intellectual disability-short stature-overweight syndrome.
• BP4: Computational evidence support a benign effect (MetaRNN=0.20471242).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
THOC2	NM_001081550.2	c.4646A>G	p.Lys1549Arg	missense_variant	Exon 36 of 39	ENST00000245838.13	NP_001075019.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
THOC2	ENST00000245838.13	c.4646A>G	p.Lys1549Arg	missense_variant	Exon 36 of 39	5	NM_001081550.2	ENSP00000245838.8
THOC2	ENST00000355725.8	c.4646A>G	p.Lys1549Arg	missense_variant	Exon 36 of 39	5		ENSP00000347959.4
THOC2	ENST00000491737.5	c.4301A>G	p.Lys1434Arg	missense_variant	Exon 32 of 34	5		ENSP00000419795.1
THOC2	ENST00000441692.5	c.1028A>G	p.Lys343Arg	missense_variant	Exon 7 of 10	5		ENSP00000415211.1
THOC2	ENST00000448128.5	c.431A>G	p.Lys144Arg	missense_variant	Exon 6 of 9	5		ENSP00000397317.1
THOC2	ENST00000416618.5	c.413A>G	p.Lys138Arg	missense_variant	Exon 5 of 8	5		ENSP00000415244.1
THOC2	ENST00000455053.5	c.125A>G	p.Lys42Arg	missense_variant	Exon 1 of 4	3		ENSP00000402168.1
THOC2	ENST00000432353.5	n.*888A>G		non_coding_transcript_exon_variant	Exon 6 of 9	1		ENSP00000415947.1
THOC2	ENST00000432353.5	n.*888A>G		3_prime_UTR_variant	Exon 6 of 9	1		ENSP00000415947.1

Frequencies

GnomAD3 genomes Cov.: 22

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 22

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: no assertion criteria provided

Submissions by phenotype

X-linked intellectual disability-short stature-overweight syndrome Uncertain:1

Jan 10, 2019

Sydney Children's Hospital, SCHN

Significance: Uncertain significance

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.091
BayesDel_addAF	Benign	-0.16	T
BayesDel_noAF	Benign	-0.46
CADD	Benign	22
DANN	Uncertain	0.99
DEOGEN2	Benign	0.034	T;.;.;.;T;T
FATHMM_MKL	Uncertain	0.88	D
LIST_S2	Uncertain	0.94	D;D;D;D;.;D
M_CAP	Benign	0.0049	T
MetaRNN	Benign	0.20	T;T;T;T;T;T
MetaSVM	Benign	-0.99	T
MutationAssessor	Benign	0.55	N;.;.;.;N;.
PhyloP100		3.7
PrimateAI	Uncertain	0.68	T
PROVEAN	Benign	-0.52	N;.;D;N;N;N
REVEL	Benign	0.23
Sift	Benign	0.24	T;.;T;T;T;T
Sift4G	Benign	0.60	T;T;T;D;T;T
Polyphen		0.0050	B;.;.;.;B;.
Vest4		0.070
MutPred		0.21		Loss of ubiquitination at K1549 (P = 0.027);.;.;.;Loss of ubiquitination at K1549 (P = 0.027);.;
MVP		0.43
MPC		0.86
ClinPred		0.60	D
GERP RS		4.6
PromoterAI		-0.077	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		2.8
Varity_R		0.19
gMVP		0.039
Mutation Taster		=86/14	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs1603229932; hg19: chrX-122747281;