12-114385521-C-T

Variant summary

Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PM1 PM2 PM5 PP3_Strong PP5_Very_Strong

The NM_181486.4(TBX5):c.710G>A(p.Arg237Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000657 in 152,148 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R237W) has been classified as Pathogenic.

• Frequency: Genomes: 𝑓 0.0000066 (0 hom., cov: 32)
• Consequence: TBX5 NM_181486.4 missense
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:8
• Conservation: PhyloP100: 7.48

Genes affected

TBX5 (HGNC:11604): (T-box transcription factor 5) This gene is a member of a phylogenetically conserved family of genes that share a common DNA-binding domain, the T-box. T-box genes encode transcription factors involved in the regulation of developmental processes. This gene is closely linked to related family member T-box 3 (ulnar mammary syndrome) on human chromosome 12. The encoded protein may play a role in heart development and specification of limb identity. Mutations in this gene have been associated with Holt-Oram syndrome, a developmental disorder affecting the heart and upper limbs. Several transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Pathogenic. Variant got 18 ACMG points.

• PM1: In a hotspot region, there are 4 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 2 benign, 7 uncertain in NM_181486.4
• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr12-114385522-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 7995.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.963
• PP5: Variant 12-114385521-C-T is Pathogenic according to our data. Variant chr12-114385521-C-T is described in ClinVar as [Likely_pathogenic]. Clinvar id is 7993.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr12-114385521-C-T is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TBX5	NM_181486.4	c.710G>A	p.Arg237Gln	missense_variant	7/9	ENST00000405440.7
TBX5	NM_000192.3	c.710G>A	p.Arg237Gln	missense_variant	7/9
TBX5	NM_080717.4	c.560G>A	p.Arg187Gln	missense_variant	6/8
TBX5	XM_017019912.2	c.758G>A	p.Arg253Gln	missense_variant	7/9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TBX5	ENST00000405440.7	c.710G>A	p.Arg237Gln	missense_variant	7/9	1	NM_181486.4	P1
TBX5	ENST00000310346.8	c.710G>A	p.Arg237Gln	missense_variant	7/9	1		P1
TBX5	ENST00000349716.9	c.560G>A	p.Arg187Gln	missense_variant	6/8	1
TBX5	ENST00000526441.1	c.710G>A	p.Arg237Gln	missense_variant	6/7	1

Frequencies

GnomAD3 genomes AF: 0.00000657 AC: 1 AN: 152148 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.0000241

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 Cov.: 31

GnomAD4 genome AF: 0.00000657 AC: 1 AN: 152148 Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1 AN XY: 74312

Gnomad4 AFR AF: 0.0000241

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: 0.00

Gnomad4 OTH AF: 0.00

Alfa AF: 0.0000688 Hom.: 0

Bravo AF: 0.00000378

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:8

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Holt-Oram syndrome Pathogenic:5

Pathogenic, criteria provided, single submitter	clinical testing	Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center	Jan 19, 2023	PS3, PM1, PM5, PP3, PS4_supporting -
Pathogenic, no assertion criteria provided	literature only	OMIM	Mar 16, 1999	- -
Pathogenic, criteria provided, single submitter	clinical testing	Fulgent Genetics, Fulgent Genetics	Dec 13, 2021	- -
Pathogenic, no assertion criteria provided	clinical testing	Centre de Biologie Pathologie Génétique, Centre Hospitalier Universitaire de Lille	Jun 14, 2018	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Apr 12, 2013	The Arg237Gln variant in TBX5 has been reported in two individuals with Holt-Ora m syndrome and segregated with disease in one affected relative (Basson 1997, Ba sson 1999). This variant has not been identified in large population studies, bu t is listed in dbSNP without frequency information (rs104894378). The TBX5 gene encodes a transcription factor and the variant is located in the DNA binding dom ain and functional studies indicate that it affects protein function (Ghosh 2001 , Hiroi 2001, Fan 2003, Fan 2009, Stirnimann 2010, Wang 2011). Computational ana lyses (biochemical amino acid properties, conservation, AlignGVGD, PolyPhen2, an d SIFT) also support that this variant may impact the protein as does the presen ce of other variants at this position that have been detected in individuals wit h Holt Oram syndrome (Arg237Pro, Arg237Trp; Basson 1999, Boogerd 2010). In summa ry, the Arg237Gln variant is likely pathogenic, though additional studies are re quired to fully establish its clinical significance. -

not provided Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

GeneDx

Dec 21, 2021

In vitro functional studies demonstrated a damaging effect through reduced DNA-binding activity, reduced transcriptional activation, and failure to act with NKX2.5 in transcriptional activation in comparison to wild-type (Fan et al., 2003; Zhou et al., 2015); Not observed at significant frequency in large population cohorts (Lek et al., 2016); This variant is associated with the following publications: (PMID: 28337273, 20519243, 12499378, 19648116, 28164238, 30552424, 20450920, 11431700, 21897873, 12789647, 10077612, 32449309, 8988165, 25986147, 25680289, 11555635) -

Aortic valve disease 2 Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Invitae

Nov 24, 2023

This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 237 of the TBX5 protein (p.Arg237Gln). This variant is present in population databases (rs104894378, gnomAD 0.01%). This missense change has been observed in individual(s) with Holt-Oram syndrome (PMID: 8988165, 12789647). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 7993). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on TBX5 protein function. Experimental studies have shown that this missense change affects TBX5 function (PMID: 11555635, 12499378). This variant disrupts the p.Arg237 amino acid residue in TBX5. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 10077612, 12499378, 12789647, 20519243). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic. -

Cardiovascular phenotype Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Apr 21, 2023

The p.R237Q variant (also known as c.710G>A), located in coding exon 6 of the TBX5 gene, results from a G to A substitution at nucleotide position 710. The arginine at codon 237 is replaced by glutamine, an amino acid with highly similar properties. This variant has been identified in multiple individuals with clinical diagnoses of Holt-Oram syndrome (Basson CT et al. Nat. Genet., 1997 Jan;15:30-5; Debeer P et al. Clin. Orthop. Relat. Res., 2007 Sep;462:20-6; Vanlerberghe C et al. Eur. J. Hum. Genet., 2019 03;27:360-368). Functional studies suggest that this alteration may affect TBX5 binding affinity to other transcription factors (Ghosh TK et al. Hum. Mol. Genet., 2001 Sep;10:1983-94; Fan C et al. J. Biol. Chem., 2003 Mar;278:8780-5). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Based on the majority of available evidence to date, this variant is likely to be pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	1.0
BayesDel_addAF	Pathogenic	0.47	D
BayesDel_noAF	Pathogenic	0.43
Cadd	Pathogenic	33
Dann	Pathogenic	1.0
Eigen	Pathogenic	0.93
Eigen_PC	Pathogenic	0.86
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Pathogenic	0.99	D;.;D;D
M_CAP	Pathogenic	0.30	D
MetaRNN	Pathogenic	0.96	D;D;D;D
MetaSVM	Pathogenic	1.0	D
MutationTaster	Benign	1.0	A;A;A;A
PrimateAI	Pathogenic	0.89	D
PROVEAN	Uncertain	-3.5	D;D;D;D
REVEL	Pathogenic	0.92
Sift	Pathogenic	0.0	D;D;D;D
Sift4G	Pathogenic	0.0	D;D;D;D
Polyphen		1.0	.;D;D;D
Vest4		0.98
MutPred		0.86		.;Gain of ubiquitination at K234 (P = 0.0398);Gain of ubiquitination at K234 (P = 0.0398);Gain of ubiquitination at K234 (P = 0.0398);
MVP		0.99
MPC		2.0
ClinPred		1.0	D
GERP RS		5.3
Varity_R		0.96
gMVP		0.87

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

Publications

LitVar

Other links and lift over

dbSNP: rs104894378; hg19: chr12-114823326;