rs2531693353 — HSD17B4 c.715-1G>A (splice acceptor)

HSD17B4 c.715-1G>A — A Splice Variant That Silences the Peroxisome's Fat-Burning Engine

The peroxisome is a cellular organelle dedicated in part to processing the fatty acids that mitochondria cannot — very long chains (more than 20 carbons), branched-chain fatty acids such as phytanic acid, and the bile acid precursors derived from cholesterol. D-bifunctional protein (DBP), encoded by HSD17B4, performs two sequential steps in this peroxisomal beta-oxidation¹¹ peroxisomal beta-oxidation
The peroxisomal beta-oxidation spiral shortens very long-chain and branched fatty acids by two carbons per cycle, generating acetyl-CoA and passing the shortened chain to mitochondria for complete oxidation. DBP catalyses the second (hydratase) and third (dehydrogenase) reactions of each cycle pathway. When DBP fails, these substrates accumulate to toxic levels in the nervous system, gonads, and other tissues.

The c.715-1G>A variant destroys the canonical splice acceptor site at the boundary of intron 9 and exon 10. This is not a subtle regulatory tweak — it eliminates a signal the spliceosome depends on to excise intron 9 cleanly. The result is aberrant splicing²² aberrant splicing
Splice acceptor variants at the invariant AG dinucleotide of an intron typically cause exon skipping, intron retention, or activation of cryptic splice sites — all of which produce frameshifted or truncated transcripts that are degraded by nonsense-mediated decay or yield a non-functional protein, essentially silencing that copy of HSD17B4.

The Mechanism

The splice acceptor at the 3′ end of an intron is defined by the invariant AG dinucleotide. The c.715-1G>A change replaces the G at position −1 of the intron 9 acceptor — the last nucleotide before the exon begins. This position is part of the [polypyrimidine-tract/AG motif | The spliceosomal U2AF complex recognises the polypyrimidine tract and the invariant AG to position the 3′ splice site. Even a single nucleotide change at the −1G position can completely abolish recognition] that the spliceosome recognises. Disrupting it prevents correct intron removal; the downstream exon is skipped or the intron is retained, and the altered transcript is either degraded by [nonsense-mediated decay | NMD is a cellular surveillance mechanism that degrades mRNAs containing premature stop codons — including those produced by exon skipping with frameshift] or produces a severely truncated, inactive protein. Because DBP is a bifunctional enzyme, loss of either catalytic domain blocks the entire beta-oxidation of very long-chain fatty acids, causing accumulation of C26:0, pristanic acid, and [bile acid intermediates | Di- and trihydroxycholestanoic acid (DHCA and THCA) are intermediates in bile acid synthesis that require peroxisomal oxidation by DBP to become chenodeoxycholic and cholic acid. In DBP deficiency these intermediates accumulate in plasma and urine] in plasma and tissues.

The Evidence

The association of HSD17B4 null alleles with fatal peroxisomal disease has been established across decades of case series and biochemical studies. Ferdinandusse et al. 2006 characterised 110 patients with DBP deficiency, identifying 61 distinct mutations³³ Ferdinandusse et al. 2006 characterised 110 patients with DBP deficiency, identifying 61 distinct mutations
Ferdinandusse et al. Mutational spectrum of D-bifunctional protein deficiency and structure-based genotype-phenotype analysis. Am J Hum Genet. 2006;78(1):112-24. The defining genotype-phenotype rule across this cohort: residual enzyme activity predicts survival. Patients carrying two null alleles (including splice-site variants) showed no detectable DBP activity and the most severe neonatal phenotype — hypotonia, seizures, absent psychomotor development, and death typically within the first two years of life.

The discovery that milder HSD17B4 alleles cause Perrault syndrome rather than neonatal death came from whole-exome sequencing. Pierce et al. 2010 identified the first compound heterozygous HSD17B4 family⁴⁴ Pierce et al. 2010 identified the first compound heterozygous HSD17B4 family
Pierce et al. Mutations in the DBP-deficiency protein HSD17B4 cause ovarian dysgenesis, hearing loss, and ataxia of Perrault syndrome. Am J Hum Genet. 2010;87(2):282-288: two sisters with sensorineural hearing loss, primary ovarian insufficiency, and ataxia — none of whom had the catastrophic neonatal course. Their mutations reduced but did not abolish DBP activity. This established that heterozygous carriage of one null allele (like a splice-site variant) paired with one hypomorphic allele produces a survivable but multisystem disorder. A splice-site null paired with a second null allele, by contrast, predicts a severe neonatal presentation.

McMillan et al. 2012 described a fourth clinical subtype (Type IV)⁵⁵ McMillan et al. 2012 described a fourth clinical subtype (Type IV) in two brothers with adult-onset cerebellar ataxia, peripheral neuropathy, and hearing loss — but normal plasma VLCFA levels. Their compound heterozygous mutations each reduced but did not abolish a single catalytic domain, leaving enough combined activity to avoid neonatal disease while producing progressive neurodegeneration in adulthood. This case underscores that negative plasma VLCFA screening does not exclude HSD17B4-deficiency when one allele is a hypomorph.

Werner et al. 2022 (PMID 34623748)⁶⁶ Werner et al. 2022 (PMID 34623748) reported a neonate with two HSD17B4 splice variants confirmed by RNA sequencing to cause exon 14 skipping, documenting virtually absent DBP activity in fibroblasts and an expanded phenotype that included persistent hypoglycemia — a then-novel finding that broadens the clinical spectrum.

Practical Actions

For individuals heterozygous for c.715-1G>A: carrier status is clinically silent but carries a 25% risk of an affected child if a partner also carries a pathogenic HSD17B4 allele. Genetic counselling and partner testing are the actionable steps. Carrier status alone does not cause accumulation of VLCFA or any known biochemical abnormality.

For individuals who are compound heterozygous (one c.715-1G>A allele plus one additional pathogenic allele): the clinical picture depends critically on the second allele's residual activity. Genetic counselling, metabolic specialist referral, and biochemical testing (plasma VLCFA, pristanic acid, bile acid intermediates; fibroblast DBP enzyme assay if plasma is normal) are the cornerstones of diagnosis. No disease-modifying therapies exist; management is supportive.

Interactions

This variant functions as a null allele at the HSD17B4 locus. Its clinical consequences depend entirely on the genotype at the second allele (compound heterozygosity is the rule for affected patients, since homozygous null variants at HSD17B4 are compatible with survival only in the case of residual activity from other mechanisms). Related SNPs already in the GeneOps database include rs137853096 (Gly16Ser, dehydrogenase domain) and rs137853097 (Asn457Tyr, hydratase domain) — both pathogenic missense variants in HSD17B4 that can compound with this splice allele.