Naming deletion resulting in premature stop gained mutation
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3.2 years ago

I am trying to name a deletion but am stumped. The deletion occurs within a protein coding sequence and is 171 BP long.

ATGTTTAGATTGTCAGTCTTAGTTCTGAACTTACTCCTTGTTAGCCATGAATTCTCGGCAGGAACCGCGAAAATTGAAATTCAGCCATTACCTGCCCTATGCAACGGATACTGCTTCCCCACCCTGAAGCCAGTTATGGAGTATGTTGCTATCCACCAGGACAAATGGAATACTTGTACGGAAATATTAGCGAACGAAGCCCGCAAGGATCAGATCCAGTTGAATATCCAGCTGGATGCCTTGAAAGCAGACGTTTCCAACATAAAGGCATCGCAGCTGTCAAAGGATGAGAAGCTGGACAGGATGGAGCGAGAGCAGTTTGCCATGCATGAATCTTTGGAGACCATCAATCGGTATCTTACAGTGAAACTGGACAGAACGAAATTGCAGCTTGAGGCGATCAAAAACACAATGGATTATATGAAGGCCCAAATGGATGGCTATTTCTCAGCCATAAATGGAGTTCAATGCCTACAGCCAGGATTTGAGAAGATAGGCGATAGATATTTTTACATCGAAGAAGATGTTGAGCTAAATTGGCTGGATGCTCAGGCCAAATGTCGTCGAATGGGAGGTCACCTAGCCTCTATAAAAACTAAACAGGAGTTTGACGCAATCGTAGAGAAGCTCGATGATTCGAAATCATACT**TCCTGGGCGTCAACGAAAACACAAAAACCGGTGACTTTGTGTCTGCAGCCTCCGGAAAAAGTTGTTTGTATCACGAGTGGGGTCCTGGTGAACCCCATCACAATAATGACCAAGAGCGATGCGTTTCAATCTTGCGAAAACTCATGCATGTGGGCAATTGTACTTATGAAA**AAAGATTCATATGCCAGTATGGCATCTAG

While the deletion size is divisible by three, it starts and stops between two codons. When the deletion is removed from the sequence it creates a premature stop codon.

ATGTTTAGATTGTCAGTCTTAGTTCTGAACTTACTCCTTGTTAGCCATGAATTCTCGGCAGGAACCGCGAAAATTGAAATTCAGCCATTACCTGCCCTATGCAACGGATACTGCTTCCCCACCCTGAAGCCAGTTATGGAGTATGTTGCTATCCACCAGGACAAATGGAATACTTGTACGGAAATATTAGCGAACGAAGCCCGCAAGGATCAGATCCAGTTGAATATCCAGCTGGATGCCTTGAAAGCAGACGTTTCCAACATAAAGGCATCGCAGCTGTCAAAGGATGAGAAGCTGGACAGGATGGAGCGAGAGCAGTTTGCCATGCATGAATCTTTGGAGACCATCAATCGGTATCTTACAGTGAAACTGGACAGAACGAAATTGCAGCTTGAGGCGATCAAAAACACAATGGATTATATGAAGGCCCAAATGGATGGCTATTTCTCAGCCATAAATGGAGTTCAATGCCTACAGCCAGGATTTGAGAAGATAGGCGATAGATATTTTTACATCGAAGAAGATGTTGAGCTAAATTGGCTGGATGCTCAGGCCAAATGTCGTCGAATGGGAGGTCACCTAGCCTCTATAAAAACTAAACAGGAGTTTGACGCAATCGTAGAGAAGCTCGATGATTCGAAATCATAC**TAA**AGATTCATATGCCAGTATGGCATCTAG

How to name this deletion? I have been trying to use hgvs guidelines from this website

https://varnomen.hgvs.org/

Using the protein-based naming, I thought of p.Phe217_Glu273del* / p.Phe217_Glu273delfs* / Phe217*

I am not sure if this is correct.

hgvs variant nomenclature • 472 views
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