rs1555225344

Positions:

• chr12-114385563-G-A

Variant summary

Our verdict is Pathogenic. Variant got 16 ACMG points: 16P and 0B. PM1 PM2 PP3_Strong PP5_Very_Strong

The ENST00000405440.7(TBX5):​c.668C>T​(p.Thr223Met) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. 13/21 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★). Synonymous variant affecting the same amino acid position (i.e. T223T) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 32)
• Consequence: TBX5 ENST00000405440.7 missense
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:4
• Conservation: PhyloP100: 9.49

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 16 ACMG points.

• PM1: In a hotspot region, there are 3 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 0 benign, 2 uncertain in ENST00000405440.7
• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.95
• PP5: Variant 12-114385563-G-A is Pathogenic according to our data. Variant chr12-114385563-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 449105.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr12-114385563-G-A is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TBX5	NM_181486.4	c.668C>T	p.Thr223Met	missense_variant	7/9	ENST00000405440.7	NP_852259.1
TBX5	NM_000192.3	c.668C>T	p.Thr223Met	missense_variant	7/9		NP_000183.2
TBX5	NM_080717.4	c.518C>T	p.Thr173Met	missense_variant	6/8		NP_542448.1
TBX5	XM_017019912.2	c.716C>T	p.Thr239Met	missense_variant	7/9		XP_016875401.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TBX5	ENST00000405440.7	c.668C>T	p.Thr223Met	missense_variant	7/9	1	NM_181486.4	ENSP00000384152	P1
TBX5	ENST00000310346.8	c.668C>T	p.Thr223Met	missense_variant	7/9	1		ENSP00000309913	P1
TBX5	ENST00000349716.9	c.518C>T	p.Thr173Met	missense_variant	6/8	1		ENSP00000337723
TBX5	ENST00000526441.1	c.668C>T	p.Thr223Met	missense_variant	6/7	1		ENSP00000433292

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:4

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Holt-Oram syndrome Pathogenic:2

Likely pathogenic, no assertion criteria provided	clinical testing	Centre de Biologie Pathologie Génétique, Centre Hospitalier Universitaire de Lille	Jun 14, 2018	- -
Pathogenic, criteria provided, single submitter	clinical testing	Victorian Clinical Genetics Services, Murdoch Childrens Research Institute	Jul 17, 2023	Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0103 - Loss of function and gain of function are known mechanisms of disease in this gene and are associated with Holt-Oram syndrome (MIM#142900). Variants resulting in a premature termination codon have a loss of function effect, while both loss- and gain of function have been demonstrated by missense variants (PMID: 18451335). Dominant negative has also been suggested as a mechanism in individuals with severe congenital heart disease (PMID: 30552424). (I) 0107 - This gene is associated with autosomal dominant disease. (I) 0112 - The condition associated with this gene has incomplete penetrance (PMID: 30552424). (I) 0200 - Variant is predicted to result in a missense amino acid change from threonine to methionine. (I) 0251 - This variant is heterozygous. (I) 0301 - Variant is absent from gnomAD (both v2 and v3). (SP) 0501 - Missense variant consistently predicted to be damaging by multiple in silico tools and very highly conserved with a moderate amino acid change. 0600 - Variant is located in the annotated T-box domain (DECIPHER). (I) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. This variant has been classified as likely pathogenic and pathogenic by multiple clinical diagnostic laboratories and has been reported in multiple individuals with Holt-Oram syndrome (ClinVar; PMIDs: 12789647, 29451098, 31502745). (SP) 0901 - This variant has strong evidence for segregation with disease. This variant has been shown to segregate in five affected individuals across two unrelated families (PMID: 12789647). (SP) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign -

Aortic valve disease 2 Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Aug 24, 2023

This sequence change replaces threonine, which is neutral and polar, with methionine, which is neutral and non-polar, at codon 223 of the TBX5 protein (p.Thr223Met). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with Holt-Oram Syndrome (PMID: 12789647, 16183809). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 449105). 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) performed at Invitae indicates that this missense variant is not expected to disrupt TBX5 protein function. For these reasons, this variant has been classified as Pathogenic. -

not provided Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

GeneDx

Feb 07, 2022

Published functional studies demonstrate that T223M interferes with the normal DNA-binding of the TBX5 protein (Stirnimann et al., 2010; Darwich et al., 2017; Markunas et al., 2021); 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; This variant is associated with the following publications: (PMID: 25680289, 24343878, 15355425, 25263169, 15710732, 16183809, 12789647, 31502745, 30552424, 26926761, 20450920, 33369127, 28164238, 34917776, 27535533) -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	1.0
BayesDel_addAF	Pathogenic	0.48	D
BayesDel_noAF	Pathogenic	0.45
CADD	Pathogenic	33
DANN	Pathogenic	1.0
DEOGEN2	Pathogenic	0.96	.;D;D;.
Eigen	Pathogenic	1.1
Eigen_PC	Pathogenic	0.99
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Pathogenic	0.99	D;.;D;D
M_CAP	Pathogenic	0.55	D
MetaRNN	Pathogenic	0.95	D;D;D;D
MetaSVM	Pathogenic	1.1	D
MutationAssessor	Pathogenic	3.8	.;H;H;H
MutationTaster	Benign	1.0	D;D;D;D
PrimateAI	Pathogenic	0.92	D
PROVEAN	Pathogenic	-5.5	D;D;D;D
REVEL	Pathogenic	0.96
Sift	Pathogenic	0.0	D;D;D;D
Sift4G	Pathogenic	0.0	D;D;D;D
Polyphen		1.0	.;D;D;D
Vest4		0.80
MutPred		0.83		.;Gain of catalytic residue at Q218 (P = 0.0115);Gain of catalytic residue at Q218 (P = 0.0115);Gain of catalytic residue at Q218 (P = 0.0115);
MVP		0.99
MPC		1.9
ClinPred		1.0	D
GERP RS		5.5
Varity_R		0.93
gMVP		0.82

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

LitVar

Other links and lift over

dbSNP: rs1555225344; hg19: chr12-114823368; COSMIC: COSV100092545;