12-114385476-C-T

Variant names:

• chr12-114385476-C-T
• rs863223776
• NM_181486.4:c.755G>A

Variant summary

Our verdict is Pathogenic. The variant received 10 ACMG points: 10P and 0B. PM2 PM5 PP3_Strong PP5_Moderate

The NM_181486.4(TBX5):​c.755G>A​(p.Ser252Asn) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 3/3 splice prediction tools predicting alterations to normal splicing. 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. S252I) has been classified as Likely pathogenic.

• Frequency: Genomes: not found (cov: 32)
• Consequence: TBX5 NM_181486.4 missense, splice_region
• Scores: Splicing: ADA: 1.000
• Clinical Significance: Likely pathogenic criteria provided, single submitter P:2
• Conservation: PhyloP100: 7.48
• Publications: 6 publications found

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]

TBX5 Gene-Disease associations (from GenCC):

• Holt-Oram syndrome

  Inheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: ClinGen, Labcorp Genetics (formerly Invitae), Orphanet, G2P, Ambry Genetics
• heart conduction disease

  Inheritance: AD Classification: MODERATE Submitted by: Genomics England PanelApp

ACMG classification

Our verdict: Pathogenic. The variant received 10 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr12-114385476-C-A is described in ClinVar as Pathogenic/Likely_pathogenic. ClinVar VariationId is 411099.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• PP3: Splicing predictors support a deleterious effect. Scorers claiming Pathogenic: dbscSNV1_ADA, dbscSNV1_RF, max_spliceai. No scorers claiming Uncertain. No scorers claiming Benign.
• PP5: Variant 12-114385476-C-T is Pathogenic according to our data. Variant chr12-114385476-C-T is described in ClinVar as Likely_pathogenic. ClinVar VariationId is 213819.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TBX5	NM_181486.4	c.755G>A	p.Ser252Asn	missense_variant, splice_region_variant	Exon 7 of 9	ENST00000405440.7	NP_852259.1
TBX5	NM_000192.3	c.755G>A	p.Ser252Asn	missense_variant, splice_region_variant	Exon 7 of 9		NP_000183.2
TBX5	NM_080717.4	c.605G>A	p.Ser202Asn	missense_variant, splice_region_variant	Exon 6 of 8		NP_542448.1
TBX5	XM_017019912.2	c.803G>A	p.Ser268Asn	missense_variant, splice_region_variant	Exon 7 of 9		XP_016875401.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TBX5	ENST00000405440.7	c.755G>A	p.Ser252Asn	missense_variant, splice_region_variant	Exon 7 of 9	1	NM_181486.4	ENSP00000384152.3
TBX5	ENST00000310346.8	c.755G>A	p.Ser252Asn	missense_variant, splice_region_variant	Exon 7 of 9	1		ENSP00000309913.4
TBX5	ENST00000349716.9	c.605G>A	p.Ser202Asn	missense_variant, splice_region_variant	Exon 6 of 8	1		ENSP00000337723.5
TBX5	ENST00000526441.1	c.755G>A	p.Ser252Asn	missense_variant, splice_region_variant	Exon 6 of 7	1		ENSP00000433292.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

Alfa AF: 0.00000535 Hom.: 0

ClinVar

Significance: Likely pathogenic

Submissions summary: Pathogenic:2

Revision: criteria provided, single submitter

Submissions by phenotype

TBX5-related disorder Pathogenic:1

Aug 01, 2024

PreventionGenetics, part of Exact Sciences

Significance: Likely pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

The TBX5 c.755G>A variant is predicted to result in the amino acid substitution p.Ser252Asn. To our knowledge, this variant has not been reported in the literature or in a large population database, indicating this variant is rare. This variant has been confirmed de novo in an individual with TBX5-related disorder (Internal Data, PreventionGenetics). A different substitution affecting the same amino acid (p.Ser252Ile) has been in association with Holt-Oram syndrome (Fan et al. 2003. PubMed ID: 12499378; Fan et al. 2009. PubMed ID: 19648116). Taken together, the c.755G>A (p.Ser252Asn) variant is interpreted as likely pathogenic. -

not provided Pathogenic:1

Feb 08, 2024

GeneDx

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Alters the last nucleotide of the exon and is predicted to destroy the splice donor site and result in aberrant splicing, although in the absence of functional evidence the actual effect of this sequence change is unknown; Not observed at significant frequency in large population cohorts (gnomAD); Has not been previously published as pathogenic or benign to our knowledge -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.51
BayesDel_addAF	Uncertain	0.019	T
BayesDel_noAF	Benign	-0.21
CADD	Pathogenic	31
DANN	Uncertain	1.0
DEOGEN2	Benign	0.35	.;T;T;.
Eigen	Uncertain	0.48
Eigen_PC	Uncertain	0.55
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Uncertain	0.95	D;.;D;D
M_CAP	Uncertain	0.12	D
MetaRNN	Uncertain	0.65	D;D;D;D
MetaSVM	Uncertain	0.12	D
MutationAssessor	Uncertain	2.2	.;M;M;M
PhyloP100		7.5
PrimateAI	Pathogenic	0.86	D
PROVEAN	Benign	-1.2	N;N;N;N
REVEL	Uncertain	0.42
Sift	Benign	0.046	D;D;D;T
Sift4G	Benign	0.12	T;T;T;T
Polyphen		0.92, 0.20	.;P;P;B
Vest4		0.68
MutPred		0.27		.;Loss of phosphorylation at S252 (P = 0.0182);Loss of phosphorylation at S252 (P = 0.0182);Loss of phosphorylation at S252 (P = 0.0182);
MVP		0.76
MPC		1.4
ClinPred		0.97	D
GERP RS		5.3
Varity_R		0.34
gMVP		0.66
Mutation Taster		=1/99	disease causing (ClinVar)

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	1.0
SpliceAI score (max)		0.80		Details are displayed if max score is > 0.2
DS_DL_spliceai		0.80		Position offset: 0

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

Other links and lift over

dbSNP: rs863223776; hg19: chr12-114823281;