rs199422117

Positions:

chr7-140015731-G-A

Variant summary

Our verdict is Likely benign. Variant got -1 ACMG points: 4P and 5B. PM1PP3PP5BP4BS2

The NM_001061.7(TBXAS1):c.1235G>A(p.Arg412Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000356 in 1,613,278 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

Frequency

Genomes: 𝑓 0.00021 ( 0 hom., cov: 33)

Exomes 𝑓: 0.00037 ( 7 hom. )

Consequence

TBXAS1
NM_001061.7 missense

Scores

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:7U:5

Conservation

PhyloP100: 8.60

Variant links:

Genes affected

TBXAS1 (HGNC:11609): (thromboxane A synthase 1) This gene encodes a member of the cytochrome P450 superfamily of enzymes. The cytochrome P450 proteins are monooxygenases which catalyze many reactions involved in drug metabolism and synthesis of cholesterol, steroids and other lipids. However, this protein is considered a member of the cytochrome P450 superfamily on the basis of sequence similarity rather than functional similarity. This endoplasmic reticulum membrane protein catalyzes the conversion of prostglandin H2 to thromboxane A2, a potent vasoconstrictor and inducer of platelet aggregation. The enzyme plays a role in several pathophysiological processes including hemostasis, cardiovascular disease, and stroke. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2008]

TBXAS1 links:

TBXAS1 (HGNC:):

TBXAS1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -1 ACMG points.

PM1

In a mutagenesis_site Loss of thromboxane-A synthase activity. Decreased heme-binding. (size 0) in uniprot entity THAS_HUMAN

PP3

Multiple lines of computational evidence support a deleterious effect 7: AlphaMissense, BayesDel_noAF, Cadd, Dann, Eigen, phyloP100way_vertebrate, REVEL [when max_spliceai, FATHMM_MKL, MetaRNN, MutationTaster was below the threshold]

PP5

Variant 7-140015731-G-A is Pathogenic according to our data. Variant chr7-140015731-G-A is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 11889.We mark this variant Likely_pathogenic, oryginal submissions are: {Uncertain_significance=4, Pathogenic=1, Likely_pathogenic=3}. Variant chr7-140015731-G-A is described in Lovd as [Pathogenic].

BP4

Computational evidence support a benign effect (MetaRNN=0.029645413). . Strength limited to SUPPORTING due to the PP5.

BS2

High Homozygotes in GnomAdExome4 at 7 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TBXAS1	NM_001061.7 linkuse as main transcript	c.1235G>A	p.Arg412Gln	missense_variant	11/13	ENST00000448866.7	NP_001052.3	P24557-1Q53F23

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TBXAS1	ENST00000448866.7 linkuse as main transcript	c.1235G>A	p.Arg412Gln	missense_variant	11/13	1	NM_001061.7	ENSP00000402536.3		P24557-1

Frequencies

GnomAD3 genomes

AF:

0.000210

AC:

AN:

152212

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0000654

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.00620

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.000833

AC:

208

AN:

249760

Hom.:

AF XY:

0.00110

AC XY:

149

AN XY:

135192

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.000163

Gnomad SAS exome

AF:

0.00660

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000266

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.000372

AC:

543

AN:

1460948

Hom.:

Cov.:

AF XY:

0.000513

AC XY:

373

AN XY:

726802

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.0000756

Gnomad4 SAS exome

AF:

0.00559

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0000153

Gnomad4 OTH exome

AF:

0.000629

GnomAD4 genome

AF:

0.000210

AC:

AN:

152330

Hom.:

Cov.:

AF XY:

0.000349

AC XY:

AN XY:

74488

show subpopulations

Gnomad4 AFR

AF:

0.00

Gnomad4 AMR

AF:

0.0000653

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.00621

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.00

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.000193

Hom.:

Bravo

AF:

0.0000302

ExAC

AF:

0.000865

AC:

105

Asia WGS

AF:

0.00260

AC:

AN:

3478

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:7Uncertain:5

Revision: criteria provided, conflicting classifications

LINK: link

Submissions by phenotype

Ghosal hematodiaphyseal dysplasia

Pathogenic:5Uncertain:4

Uncertain significance, no assertion criteria provided	curation	Reproductive Health Research and Development, BGI Genomics	Jan 06, 2020	NM_001061.4:c.1238G>A in the TBXAS1 gene has an allele frequency of 0.007 in South Asian subpopulation in the gnomAD database. It has been detected in homozygous state in one consanguineous family with Ghosal hematodiaphyseal dysplasia syndrome (PMID: 18264100). We interpret it as variant of uncertain significance (VUS). ACMG/AMP criteria applied: PP4. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India	-	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Neuberg Centre For Genomic Medicine, NCGM	-	A variant in the next codon (c.1376G>A) has been previously reported as variant of uncertain significance in consanguineous family with Ghosal hematodiaphyseal dysplasia syndrome (David Genevie`ve, 2008) and has been submitted to ClinVar as Variant of Uncertain Significance. The missense variant is predicted to be tolerated by both SIFT or PolyPhen2. The nucleotide is not conserved according to a GERP++ and PhyloP analysis of 100 vertebrates. The variant is observed in 0.0035% alleles in gnomAD Exomes with 1 individual carrying it in a homozygous state and hence it has been classified as a variant of Uncertain Significance. -
Pathogenic, no assertion criteria provided	literature only	OMIM	Mar 01, 2008	- -
Likely pathogenic, no assertion criteria provided	clinical testing	Allergy Immunology Laboratory, Postgraduate Institute of Medical Education and Research, Chandigarh	Dec 21, 2020	c.1376G>A: In-silico predictions for this variant are damaging and probably damaging. Two other missense variants affecting the same codon have been previously reported with Ghosal hematodiaphyseal syndrome. The variant was present in a heterozygous state with another variant on the other allele c.125_138del; p.Lys42ThrfsTer47. Additionally it was present in homozygous state in another patient. -
Uncertain significance, criteria provided, single submitter	clinical testing	Suma Genomics	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	Mendelics	May 04, 2022	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center	Mar 25, 2024	- -
Pathogenic, no assertion criteria provided	clinical testing	Biochemical Molecular Genetic Laboratory, King Abdulaziz Medical City	Aug 07, 2020	- -

not provided

Pathogenic:2Uncertain:1

Likely pathogenic, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Feb 01, 2024	TBXAS1: PM3:Strong, PM2:Supporting, PP4, PS3:Supporting -
Uncertain significance, criteria provided, single submitter	clinical testing	GeneDx	Oct 22, 2019	In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; This variant is associated with the following publications: (PMID: 33185009, 27156553, 18264100) -
Likely pathogenic, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Dec 21, 2023	This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 413 of the TBXAS1 protein (p.Arg413Gln). This variant is present in population databases (rs199422117, gnomAD 0.6%), and has an allele count higher than expected for a pathogenic variant. This missense change has been observed in individual(s) with Ghosal hematodiaphyseal dysplasia (PMID: 18264100, 27156553, 33185009, 33244729, 35395429). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 11889). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. Experimental studies have shown that this missense change affects TBXAS1 function (PMID: 8702713). In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Pathogenic

0.66

BayesDel_addAF

Uncertain

0.11

BayesDel_noAF

Pathogenic

0.40

CADD

Pathogenic

DANN

Pathogenic

1.0

DEOGEN2

Benign

0.34

.;T;.;.;T;.

Eigen

Pathogenic

0.79

Eigen_PC

Uncertain

0.61

FATHMM_MKL

Pathogenic

0.98

LIST_S2

Uncertain

0.94

D;D;.;D;.;D

M_CAP

Uncertain

0.15

MetaRNN

Benign

0.030

T;T;T;T;T;T

MetaSVM

Pathogenic

0.88

PrimateAI

Uncertain

0.52

PROVEAN

Uncertain

-3.7

D;D;.;.;.;.

REVEL

Pathogenic

0.87

Sift

Pathogenic

0.0

D;D;.;.;.;.

Sift4G

Pathogenic

0.0

D;D;.;.;.;.

Polyphen

1.0

.;.;D;D;.;.

Vest4

0.95

MVP

0.86

MPC

0.60

ClinPred

0.22

GERP RS

4.6

gMVP

0.94

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.060

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over