rs117648444 — IFNL4 Pro70Ser (P70S)

IFNL4 Pro70Ser — The Protein-Activity Modifier That Stratifies Hepatitis C Risk

Within the IFNL4 gene on chromosome 19, the major functional switch for hepatitis C risk is the rs368234815 ΔG frameshift polymorphism¹¹ rs368234815 ΔG frameshift polymorphism
the causal variant that controls whether functional IFN-λ4 protein is produced at all. But not all ΔG carriers face the same risk. A second coding variant in exon 2 — rs117648444, which swaps a proline for a serine at position 70 of the IFN-λ4 protein (p.Pro70Ser) — significantly modulates how active the resulting protein actually is. The Ser70 form (S70) is substantially weaker than the ancestral Pro70 (P70), and ΔG carriers who produce the attenuated S70 protein achieve better hepatitis C clearance outcomes than those producing the fully active P70 form. This creates a functional three-tier hierarchy for IFNL4: TT/TT (no protein) > ΔG-S70 (weak protein) > ΔG-P70 (fully active protein).

The Mechanism

rs117648444 is a missense variant²² missense variant
a coding SNP that changes a single amino acid in the protein sequence. On the IFNL4 minus strand, the coding change is c.208C>T; on the genomic plus strand (as reported in genome files), the alleles are G (reference, Pro70) and A (alternate, Ser70). The substitution of serine for proline at position 70 disrupts the local secondary structure of the IFN-λ4 protein — proline is a rigid, helix-breaking residue, while serine introduces a hydroxyl group and greater flexibility. The result is an IFN-λ4 protein with substantially lower capacity to activate downstream interferon-stimulated genes³³ interferon-stimulated genes
ISGs; hundreds of genes whose protein products directly inhibit viral replication, and reduced antiviral activity against viral challenge models.

Crucially, the A allele (Ser70) is only found on haplotypes that also carry the rs368234815 ΔG allele — it has never been observed on the TT (null) background. This means the rs117648444 variant is uninformative for TT/TT individuals (who produce no IFN-λ4 regardless), and its clinical significance is entirely confined to ΔG carriers. The three haplotypes observed in humans are: (1) IFNL4-TT with rs117648444-G (no protein); (2) IFNL4-ΔG with rs117648444-G (fully active P70 protein); and (3) IFNL4-ΔG with rs117648444-A (attenuated S70 protein).

The Evidence

The variant was characterised in Galmozzi & Aghemo 2014⁴⁴ Galmozzi & Aghemo 2014
"Nonsynonymous variant Pro70Ser (rs117648444) in IFNL4 gene identifies carriers of the rs368234815 ΔG allele with higher HCV RNA decline during the first 4 weeks of pegylated interferon and ribavirin therapy in HCV-1 patients", showing that ΔG carriers with the S70 modifier had significantly greater early viral RNA decline than ΔG-P70 carriers, approaching the response of TT/TT non-producers.

The mechanistic evidence was established by Terczynska-Dyla et al. 2014⁵⁵ Terczynska-Dyla et al. 2014
"Reduced IFNλ4 activity is associated with improved HCV clearance and reduced expression of interferon-stimulated genes" using recombinant protein assays: the S70 protein induced significantly lower intrahepatic ISG expression and had weaker antiviral activity than the P70 protein in direct comparison. The same study confirmed that, in population cohorts, individuals predicted to produce only the S70 form had better spontaneous HCV clearance rates than P70 producers — intermediate between TT/TT (best) and ΔG-P70 (worst).

A 2015 comparative analysis of IFNL4 and IFNL3 functional variants⁶⁶ comparative analysis of IFNL4 and IFNL3 functional variants
Terczynska-Dyla et al., Journal of Hepatology found that rs117648444 adds independent prognostic information beyond rs368234815 alone. In African American participants — where the ΔG allele is common and LD structure differs substantially from Europeans — rs368234815 combined with rs117648444 provided stronger association with HCV outcomes than either variant alone or than the traditional rs12979860 IL28B marker.

The clinical reach extends beyond HCV. In IFN-treated HBeAg-negative chronic hepatitis B patients⁷⁷ IFN-treated HBeAg-negative chronic hepatitis B patients
Galmozzi et al. 2018, Liver International, the combination of rs368234815 and rs117648444 genotypes strongly predicted HBsAg seroclearance at 15 years: the 15-year cumulative probability of HBsAg loss was comparable between S70 carriers and TT/TT individuals (both significantly higher than P70 producers), suggesting the same IFN-λ4 activity gradient that governs HCV outcomes also applies to hepatitis B treatment.

A 2017 study of HCV genotype 3 patients in India⁸⁸ HCV genotype 3 patients in India
Datta et al., PMID 28727946 found that failure to genotype rs117648444 causes confounding in IFNL locus association studies: tag SNPs in linkage disequilibrium with ΔG that happen to be correlated with the S70 modifier will show misleadingly strong or weak associations with treatment response depending on their LD pattern.

Practical Implications

For clinical purposes, rs117648444 is most useful as a refinement tool for ΔG carriers identified by rs368234815 genotyping. A ΔG carrier who also has the S70 modifier (rs117648444-AG or AA) faces a different prognosis than a P70 ΔG carrier (GG at this locus with ΔG at rs368234815): their treatment response profile is closer to that of TT/TT non-producers than to the worst ΔG-P70 subgroup.

For the majority of individuals who are TT/TT at rs368234815, this variant carries no clinical significance: they produce no functional IFN-λ4 regardless of what they carry at rs117648444. For individuals who have not been exposed to hepatitis C and have no ongoing risk, the variant is informationally interesting but does not require clinical action.

Interactions

rs117648444 is functionally downstream of rs368234815. The ΔG allele at rs368234815 is the prerequisite for any effect at rs117648444 — only ΔG/TT or ΔG/ΔG individuals at rs368234815 can benefit from S70 status. Among those ΔG carriers, rs117648444 sub-stratifies by protein activity: the A allele (S70) attenuates IFN-λ4 function and shifts outcomes toward the TT/TT tier. For compound genotype interpretation across both variants, see the interaction analysis in the rs368234815 entry. rs12979860 (the original "IL28B" C/T marker) is a proxy tag for the ΔG/TT distinction and does not capture the P70S modification — making combined genotyping of rs368234815 and rs117648444 the most informative approach.