diff --git a/data-pipeline/src/data_pipeline/data_types/gene.py b/data-pipeline/src/data_pipeline/data_types/gene.py
index 393d043b8..958484be7 100644
--- a/data-pipeline/src/data_pipeline/data_types/gene.py
+++ b/data-pipeline/src/data_pipeline/data_types/gene.py
@@ -111,6 +111,12 @@ def collect_gene_exons(gene_exons):
     return exons
 
 
+def reject_par_y_genes(genes_path=None):
+    genes = hl.read_table(genes_path)
+    genes = genes.filter(genes.gene_version.endswith("_PAR_Y") == hl.literal(False))
+    return genes
+
+
 ###############################################
 # Transcripts                                 #
 ###############################################
diff --git a/data-pipeline/src/data_pipeline/pipelines/genes.py b/data-pipeline/src/data_pipeline/pipelines/genes.py
index 54d9f894e..2ceddad60 100644
--- a/data-pipeline/src/data_pipeline/pipelines/genes.py
+++ b/data-pipeline/src/data_pipeline/pipelines/genes.py
@@ -24,6 +24,7 @@
     prepare_heterozygous_variant_cooccurrence_counts,
     prepare_homozygous_variant_cooccurrence_counts,
 )
+from data_pipeline.data_types.gene import reject_par_y_genes
 
 pipeline = Pipeline()
 
@@ -317,6 +318,15 @@ def annotate_with_preferred_transcript(table_path):
     },
 )
 
+pipeline.add_task(
+    "annotate_grch38_genes_step_5",
+    reject_par_y_genes,
+    "/genes/genes_grch38_annotated_5.ht",
+    {
+        "genes_path": pipeline.get_task("annotate_grch38_genes_step_4"),
+    },
+)
+
 ###############################################
 # Extract transcripts
 ###############################################
@@ -357,7 +367,7 @@ def annotate_with_preferred_transcript(table_path):
 pipeline.set_outputs(
     {
         "genes_grch37": "annotate_grch37_genes_step_5",
-        "genes_grch38": "annotate_grch38_genes_step_4",
+        "genes_grch38": "annotate_grch38_genes_step_5",
         "base_transcripts_grch37": "extract_grch37_transcripts",
         "base_transcripts_grch38": "extract_grch38_transcripts",
         "transcripts_grch37": "annotate_grch37_transcripts",