rs1554035308

Variant names:

• chr5-74696692-G-T
• rs1554035308
• NM_000521.4:c.512-1G>T

Variant summary

Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1_Moderate PM2 PP5_Very_Strong

The NM_000521.4(HEXB):​c.512-1G>T variant causes a splice acceptor, intron change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely pathogenic (★★).

• Frequency: Genomes: not found (cov: 33)
• Consequence: HEXB NM_000521.4 splice_acceptor, intron
• Scores: Splicing: ADA: 1.000
• Clinical Significance: Likely pathogenic criteria provided, multiple submitters, no conflicts P:2
• Conservation: PhyloP100: 6.25

Genes affected

HEXB (HGNC:4879): (hexosaminidase subunit beta) Hexosaminidase B is the beta subunit of the lysosomal enzyme beta-hexosaminidase that, together with the cofactor GM2 activator protein, catalyzes the degradation of the ganglioside GM2, and other molecules containing terminal N-acetyl hexosamines. Beta-hexosaminidase is composed of two subunits, alpha and beta, which are encoded by separate genes. Both beta-hexosaminidase alpha and beta subunits are members of family 20 of glycosyl hydrolases. Mutations in the alpha or beta subunit genes lead to an accumulation of GM2 ganglioside in neurons and neurodegenerative disorders termed the GM2 gangliosidoses. Beta subunit gene mutations lead to Sandhoff disease (GM2-gangliosidosis type II). Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2014]

ACMG classification

Verdict is Pathogenic. Variant got 12 ACMG points.

• PVS1: Splicing +-2 bp (donor or acceptor) variant, product NOT destroyed by NMD, known LOF gene, truncates exone, which is 0.02812687 fraction of the gene. Cryptic splice site detected, with MaxEntScore 8.3, offset of 6, new splice context is: tttactttcctcatgtttAGaga. Cryptic site results in inframe change. If cryptic site found is not functional and variant results in exon loss, it results in frameshift change.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 5-74696692-G-T is Pathogenic according to our data. Variant chr5-74696692-G-T is described in ClinVar as [Likely_pathogenic]. Clinvar id is 557184.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HEXB	NM_000521.4	c.512-1G>T		splice_acceptor_variant, intron_variant	Intron 3 of 13	ENST00000261416.12	NP_000512.2
HEXB	NM_001292004.2	c.-164-1G>T		splice_acceptor_variant, intron_variant	Intron 3 of 13		NP_001278933.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HEXB	ENST00000261416.12	c.512-1G>T		splice_acceptor_variant, intron_variant	Intron 3 of 13	1	NM_000521.4	ENSP00000261416.7
HEXB	ENST00000511181.5	c.-164-1G>T		splice_acceptor_variant, intron_variant	Intron 3 of 13	1		ENSP00000426285.1
HEXB	ENST00000510820.1	n.231-1G>T		splice_acceptor_variant, intron_variant	Intron 1 of 3	3
HEXB	ENST00000513079.5	n.577-1G>T		splice_acceptor_variant, intron_variant	Intron 3 of 5	2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 20

GnomAD4 genome Cov.: 33

ClinVar

Significance: Likely pathogenic

Submissions summary: Pathogenic:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Sandhoff disease Pathogenic:2

Aug 31, 2023

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant summary: HEXB c.512-1G>T is located in a canonical splice-site and is predicted to affect mRNA splicing resulting in a significantly altered protein due to either exon skipping, shortening, or inclusion of intronic material. Several computational tools predict a significant impact on normal splicing: Three predict the variant abolishes a canonical 3' splicing acceptor site. These three tools also predict the variant creates or strengthens a cryptic 3' acceptor site 6 nucleotides downstream of the canonical site. At least one publication reports experimental evidence that this variant affects mRNA splicing, finding that a patient with the variant expresses transcripts lacking the first 6 nucleotides of exon 4, which is predicted to result in an in-frame deletion of the G171 and L172 residues (Zampieri_2008), located in the Beta-hexosaminidase, eukaryotic type, N-terminal domain (IPR029019) of the encoded protein. The variant was absent in 247230 control chromosomes (gnomAD). c.512-1G>T has been reported in the literature in an individual affected with Sandhoff Disease (Zampieri_2008). This patient was reported as compound heterozygous with another variant (c.299G>T) predicted to have a splicing impact, and RT-PCR and sequencing analysis did not find a transcript associated with this allele, indicating it produces an unstable transcript. These data suggest that c.512-1G>T is likely associated with disease. The following publication has been ascertained in the context of this evaluation (PMID: 18758829). One submitter has cited a clinical-significance assessment for this variant to ClinVar after 2014 and has classified the variant as likely pathogenic. Based on the evidence outlined above, the variant was classified as likely pathogenic. -

Mar 12, 2018

Counsyl

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.40	D
BayesDel_noAF	Pathogenic	0.34
CADD	Pathogenic	35
DANN	Uncertain	1.0
Eigen	Pathogenic	1.2
Eigen_PC	Pathogenic	1.0
FATHMM_MKL	Pathogenic	0.99	D
GERP RS		5.7
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.94
SpliceAI score (max)		0.99		Details are displayed if max score is > 0.2
DS_AG_spliceai		0.56		Position offset: 7
DS_AL_spliceai		0.99		Position offset: 1

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

Publications

LitVar

Other links and lift over

dbSNP: rs1554035308; hg19: chr5-73992517;