NM_000520.6:c.1176G>A

Variant names:

Variant summary

Our verdict is Pathogenic. The variant received 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate

The NM_000520.6(HEXA):c.1176G>A(p.Trp392*) variant causes a stop gained change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,838 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 Pathogenic (★). Variant results in nonsense mediated mRNA decay.

Frequency

Genomes: not found (cov: 30)

Exomes 𝑓: 6.8e-7 ( 0 hom. )

Consequence

HEXA
NM_000520.6 stop_gained

Scores

Clinical Significance

Pathogenic criteria provided, single submitter P:1O:1

Conservation

PhyloP100: 7.78

Publications

5 publications found

Variant links:

Genes affected

HEXA (HGNC:4878): (hexosaminidase subunit alpha) This gene encodes a member of the glycosyl hydrolase 20 family of proteins. The encoded preproprotein is proteolytically processed to generate the alpha subunit of the lysosomal enzyme beta-hexosaminidase. This enzyme, together with the cofactor GM2 activator protein, catalyzes the degradation of the ganglioside GM2, and other molecules containing terminal N-acetyl hexosamines. Mutations in this gene lead to an accumulation of GM2 ganglioside in neurons, the underlying cause of neurodegenerative disorders termed the GM2 gangliosidoses, including Tay-Sachs disease (GM2-gangliosidosis type I). Alternative splicing results in multiple transcript variants, at least one of which encodes a preproprotein that is proteolytically processed. [provided by RefSeq, Jan 2016]

HEXA Gene-Disease associations (from GenCC):

Tay-Sachs disease
Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Myriad Women’s Health, Genomics England PanelApp, G2P, Labcorp Genetics (formerly Invitae), ClinGen

HEXA links:

ENSG00000261460 (HGNC:58304):

ENSG00000261460 links:

ENSG00000260729 (HGNC:):

ENSG00000260729 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Pathogenic. The variant received 12 ACMG points.

PVS1

Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.

PM2

Very rare variant in population databases, with high coverage;

PP5

Variant 15-72346681-C-T is Pathogenic according to our data. Variant chr15-72346681-C-T is described in CliVar as Pathogenic. Clinvar id is 3936.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr15-72346681-C-T is described in CliVar as Pathogenic. Clinvar id is 3936.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr15-72346681-C-T is described in CliVar as Pathogenic. Clinvar id is 3936.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr15-72346681-C-T is described in CliVar as Pathogenic. Clinvar id is 3936.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr15-72346681-C-T is described in CliVar as Pathogenic. Clinvar id is 3936.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr15-72346681-C-T is described in CliVar as Pathogenic. Clinvar id is 3936.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr15-72346681-C-T is described in CliVar as Pathogenic. Clinvar id is 3936.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr15-72346681-C-T is described in CliVar as Pathogenic. Clinvar id is 3936.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr15-72346681-C-T is described in CliVar as Pathogenic. Clinvar id is 3936.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr15-72346681-C-T is described in CliVar as Pathogenic. Clinvar id is 3936.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr15-72346681-C-T is described in CliVar as Pathogenic. Clinvar id is 3936.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr15-72346681-C-T is described in CliVar as Pathogenic. Clinvar id is 3936.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr15-72346681-C-T is described in CliVar as Pathogenic. Clinvar id is 3936.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr15-72346681-C-T is described in CliVar as Pathogenic. Clinvar id is 3936.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr15-72346681-C-T is described in CliVar as Pathogenic. Clinvar id is 3936.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr15-72346681-C-T is described in CliVar as Pathogenic. Clinvar id is 3936.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr15-72346681-C-T is described in CliVar as Pathogenic. Clinvar id is 3936.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr15-72346681-C-T is described in CliVar as Pathogenic. Clinvar id is 3936.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr15-72346681-C-T is described in CliVar as Pathogenic. Clinvar id is 3936.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr15-72346681-C-T is described in CliVar as Pathogenic. Clinvar id is 3936.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr15-72346681-C-T is described in CliVar as Pathogenic. Clinvar id is 3936.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr15-72346681-C-T is described in CliVar as Pathogenic. Clinvar id is 3936.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr15-72346681-C-T is described in CliVar as Pathogenic. Clinvar id is 3936.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HEXA	NM_000520.6 link	c.1176G>A	p.Trp392*	stop_gained	Exon 11 of 14	ENST00000268097.10	NP_000511.2	P06865-1A0A0S2Z3W3
HEXA	NM_001318825.2 link	c.1209G>A	p.Trp403*	stop_gained	Exon 11 of 14		NP_001305754.1	P06865H3BP20B4DVA7
HEXA	NR_134869.3 link	n.1116-356G>A		intron_variant	Intron 9 of 10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HEXA	ENST00000268097.10 link	c.1176G>A	p.Trp392*	stop_gained	Exon 11 of 14	1	NM_000520.6	ENSP00000268097.6		P06865-1
ENSG00000260729	ENST00000379915.4 link	n.413-356G>A		intron_variant	Intron 3 of 15	2		ENSP00000478716.1		A0A087WUJ7

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

6.84e-7

AC:

AN:

1461838

Hom.:

Cov.:

AF XY:

0.00000138

AC XY:

AN XY:

727218

show subpopulations

African (AFR)

AF:

0.0000299

AC:

AN:

33478

American (AMR)

AF:

0.00

AC:

AN:

44724

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

26136

East Asian (EAS)

AF:

0.00

AC:

AN:

39700

South Asian (SAS)

AF:

0.00

AC:

AN:

86256

European-Finnish (FIN)

AF:

0.00

AC:

AN:

53418

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5736

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

1112004

Other (OTH)

AF:

0.00

AC:

AN:

60386

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.625

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

Bravo

AF:

0.00000378

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1Other:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Tay-Sachs disease

Pathogenic:1Other:1

Nov 17, 2023

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Pathogenic

Review Status:criteria provided, single submitter

Collection Method:clinical testing

This sequence change creates a premature translational stop signal (p.Trp392*) in the HEXA gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in HEXA are known to be pathogenic (PMID: 1833974, 8490625). This variant is not present in population databases (gnomAD no frequency). This premature translational stop signal has been observed in individual(s) with Tay-Sachs disease (PMID: 1301958). ClinVar contains an entry for this variant (Variation ID: 3936). For these reasons, this variant has been classified as Pathogenic. -

Jan 01, 1992

OMIM

Significance:Affects

Review Status:no assertion criteria provided

Collection Method:literature only

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Pathogenic

0.63

BayesDel_noAF

Pathogenic

0.66

CADD

Pathogenic

(source)

DANN

Uncertain

1.0

Eigen

Pathogenic

0.94

Eigen_PC

Pathogenic

0.81

FATHMM_MKL

Pathogenic

1.0

PhyloP100

7.8

Vest4

0.98

GERP RS

5.9

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Mutation Taster

=0/200

disease causing (ClinVar)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over