X-123611448-C-A

Variant names:

• chrX-123611448-C-A
• NM_001081550.2:c.4746G>T

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.4746G>T​(p.Glu1582Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 22)
• Consequence: THOC2 NM_001081550.2 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.353
• Publications: 0 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=0.1895332).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
THOC2	NM_001081550.2	c.4746G>T	p.Glu1582Asp	missense_variant	Exon 37 of 39	ENST00000245838.13	NP_001075019.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
THOC2	ENST00000245838.13	c.4746G>T	p.Glu1582Asp	missense_variant	Exon 37 of 39	5	NM_001081550.2	ENSP00000245838.8
THOC2	ENST00000355725.8	c.4746G>T	p.Glu1582Asp	missense_variant	Exon 37 of 39	5		ENSP00000347959.4
THOC2	ENST00000491737.5	c.4401G>T	p.Glu1467Asp	missense_variant	Exon 33 of 34	5		ENSP00000419795.1
THOC2	ENST00000441692.5	c.1128G>T	p.Glu376Asp	missense_variant	Exon 8 of 10	5		ENSP00000415211.1
THOC2	ENST00000448128.5	c.531G>T	p.Glu177Asp	missense_variant	Exon 7 of 9	5		ENSP00000397317.1
THOC2	ENST00000416618.5	c.513G>T	p.Glu171Asp	missense_variant	Exon 6 of 8	5		ENSP00000415244.1
THOC2	ENST00000455053.5	c.225G>T	p.Glu75Asp	missense_variant	Exon 2 of 4	3		ENSP00000402168.1
THOC2	ENST00000432353.5	n.*988G>T		non_coding_transcript_exon_variant	Exon 7 of 9	1		ENSP00000415947.1
THOC2	ENST00000432353.5	n.*988G>T		3_prime_UTR_variant	Exon 7 of 9	1		ENSP00000415947.1

Frequencies

GnomAD3 genomes Cov.: 22

GnomAD4 exome Cov.: 25

GnomAD4 genome Cov.: 22

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Uncertain:1

Feb 04, 2025

GeneDx

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.096
BayesDel_addAF	Benign	0.0080	T
BayesDel_noAF	Benign	-0.23
CADD	Benign	21
DANN	Benign	0.89
DEOGEN2	Benign	0.022	T;.;.;.;T;T
FATHMM_MKL	Uncertain	0.82	D
LIST_S2	Uncertain	0.87	D;D;D;D;.;D
M_CAP	Benign	0.0089	T
MetaRNN	Benign	0.19	T;T;T;T;T;T
MetaSVM	Benign	-0.96	T
MutationAssessor	Benign	0.97	L;.;.;.;L;.
PhyloP100		0.35
PrimateAI	Pathogenic	0.79	T
PROVEAN	Benign	-0.48	N;.;D;N;N;N
REVEL	Benign	0.11
Sift	Benign	0.14	T;.;D;D;T;T
Sift4G	Benign	0.074	T;D;T;T;T;T
Polyphen		0.98	D;.;.;.;D;.
Vest4		0.22
MutPred		0.15		Loss of methylation at K1584 (P = 0.1175);.;.;.;Loss of methylation at K1584 (P = 0.1175);.;
MVP		0.58
MPC		1.7
ClinPred		0.80	D
GERP RS		2.0
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		2.8
Varity_R		0.097
gMVP		0.0088
Mutation Taster		=82/18	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.050		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

hg19: chrX-122745299; COSMIC: COSV55543569; COSMIC: COSV55543569;