We found hereditary congenital facial paralysis type 1 (HCFP1) is caused by variants that duplicate or change cis regulatory elements (cREs) controlling the neuronal expression of the GATA2 transcription factor. The single nucleotide variants (SNVs) alter a previously uncharacterized cis regulatory element (we named cRE2). A subset of these variants disrupted a consensus sequence for the COUP transcription factor family (NR2F1 and NR2F2). We performed low-input scCUT&Tag with antibodies against NR2F1 and found it bound to the predicted cRE2 sequence in embryonic mouse rhombomere 4 motor neurons in vivo. We generated an HCFP1 SNV mouse model that harbored Mm10:Chr6:88,224,892 A>G in the NR2F1 binding site (Fam5snv/snv) and found it disrupted NR2F1 binding in vivo. Overall design: scCUT&Tag (see “Single Cell CUT and Tag on 10X genomics platform” protocol from www.protocol.io) (https://www.protocols.io/view/single-cell-cut-and-tag-on-10x-genomics-platform-bqbnmsme) was performed on FAC-sorted WT and Fam5snv/snv mouse embryonic rhombomere 4 motor neurons marked by the motor neuron-specific Isl1MN-GFP transgenic reporter. Cells were collected at E10.5 (replicate 1: n=26 WT and 8 Fam5snv/snv embryos; replicate 2: n=26 WT and 16 Fam5snv/snv embryos), and processed for scCUT&Tag using an antibody against the COUP-TFI/NR2F1 transcription factor (Millipore-Sigma cat#ABE1425). Libraries were sequenced on an Illumina NextSeq 500 using a NextSeq 500/550 High Output v2.5 (75 cycles) kit (Illumina). Raw sequence data was demultiplexed, filtered and aligned using CellRanger-ATAC software (10x Genomics) to generate fastqs and peak files for deposit.