Table 3 Characteristics of the identified POMGNT1 variant in this study

Gene

HGNC symbol: POMGNT1

Ensembl version: ENSG00000085998.15

Genomic location: chr1 (hg38):46188681–46220305

Cytogenetic location: 1p34.1

Transcript coordinates

Ensembl transcript ID: ENST00000371992.1

GenBank transcript ID: NM_001243766

UniProt peptide

Q8WZA1

Identified Variant

Type: single-nucleotide variant, Zygosity: Homozygous

Variant length: 1 bp

Consequence: nonsense, stop-gained-NMD

Allele origin: germline

RefSeq: NM_001243766.2:c.74G>A:p.25W*

Alteration position

Chromosome: chr1: 46197748 C>TN/A (Assembly GRCh38)

gDNA: g.22558G>A

cDNA: cDNA.725G>A

CDS: c.74G>A

Exon: 2/23

AA: Trp25Ter

Sequence snippet

Original gDNA

GCGGAGCTGGTACCTTACC T[G]G AAGTATAAACTGACAAACC

Altered gDNA

GCGGAGCTGGTACCTTACC T[A]G AAGTATAAACTGACAAACC

Original cDNA

GCGGAGCTGGTACCTTACC T[G]G AAGTATAAACTGACAAACC

Altered cDNA

GCGGAGCTGGTACCTTACC T[A]G AAGTATAAACTGACAAACC

wt-AA sequence

wt-AA sequence: MDDWKPSPLI KPFGARKKRS WYLT[W]KYKLT

mu-AA sequence

mu-AA sequence: MDDWKPSPLI KPFGARKKRS WYLT*