12-114366188-AT-A

Position:

• chr12-114366188-AT-A

Variant summary

Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PVS1_Strong PM2 PP5_Moderate

The NM_181486.4(TBX5):​c.958del​(p.Ile320PhefsTer74) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: TBX5 NM_181486.4 frameshift
• Clinical Significance: Pathogenic criteria provided, single submitter P:1
• Conservation: PhyloP100: 2.50

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 Likely_pathogenic. Variant got 8 ACMG points.

• PVS1: Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant is located in the 3'-most 50 bp of the penultimate exon, not predicted to undergo nonsense mediated mRNA decay. Fraction of 0.385 CDS is truncated, and there are 0 pathogenic variants in the truncated region.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 12-114366188-AT-A is Pathogenic according to our data. Variant chr12-114366188-AT-A is described in ClinVar as [Pathogenic]. Clinvar id is 237218.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr12-114366188-AT-A is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TBX5	NM_181486.4	c.958del	p.Ile320PhefsTer74	frameshift_variant	8/9	ENST00000405440.7	NP_852259.1
TBX5	NM_000192.3	c.958del	p.Ile320PhefsTer74	frameshift_variant	8/9		NP_000183.2
TBX5	NM_080717.4	c.808del	p.Ile270PhefsTer74	frameshift_variant	7/8		NP_542448.1
TBX5	XM_017019912.2	c.1006del	p.Ile336PhefsTer74	frameshift_variant	8/9		XP_016875401.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TBX5	ENST00000405440.7	c.958del	p.Ile320PhefsTer74	frameshift_variant	8/9	1	NM_181486.4	ENSP00000384152	P1
TBX5	ENST00000310346.8	c.958del	p.Ile320PhefsTer74	frameshift_variant	8/9	1		ENSP00000309913	P1
TBX5	ENST00000349716.9	c.808del	p.Ile270PhefsTer74	frameshift_variant	7/8	1		ENSP00000337723
TBX5	ENST00000526441.1	c.958del	p.Ile320PhefsTer?	frameshift_variant	7/7	1		ENSP00000433292

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: criteria provided, single submitter

Submissions by phenotype

Aortic valve disease 2 Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 27, 2016

For these reasons, this variant has been classified as Pathogenic. While this particular variant has not been reported in the literature, truncating variants in TBX5 are known to be pathogenic (PMID: 16183809, 16917909). This sequence change deletes 1 nucleotide from exon 8 of the TBX5 mRNA (c.958delA), causing a frameshift at codon 320. This creates a premature translational stop signal (p.Ile320Phefs*74) and is expected to result in an absent or disrupted protein product. -

Computational scores

Source: dbNSFP v4.3

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: rs878853750; hg19: chr12-114803993;