HGVS命名之【缺失】Deletion

最近在复习HGVS命名，当做个人翻译笔记吧。

HGVS，全称是Human Genome Variation Society，人类基因组变异协会的缩写。

本周翻译的是第二部分Deletion，原文地址http://varnomen.hgvs.org/recommendations/DNA/variant/Deletion/

【缺失】Deletion

定义：与参考序列相比，一个或多个核苷酸被移除

格式：前缀（所使用的参考序列）+ . +缺失位置（范围）+del，举例：g.123_127del

要点：

①接受的参考序列包括g. m. c. n.

②缺失范围“_”前后应该为两个不同的位置，如123_126 而非 123_123

③缺失范围“_”前后应该遵循5'至3'的顺序，如123_126 而非 126_123

④遵循3'规则，但也有例外（如缺失发生在外显子与内含子交界处，且两个衔接处的碱基一致时）

举例：

NG_012232.1:g.19del (one nucleotide)

a deletion of the T at position g.19 in the sequence AGAATCACA to AGAA_CACA

NOTE: it is allowed to describe the variant as NG_012232.1:g.19delT

NG_012232.1:g.19_21del (several nucleotides)

a deletion of nucleotides g.19 to g.21 in the sequence AGAATCACA to AGAA___CA

NOTE: it is allowed to describe the variant as NG_012232.1:g.19_21delTCA  原网站错了——heyi 2017-9-6

NG_012232.1(NM_004006.1):c.183_186+48del

a deletion of nucleotides c.183 to c.186+48 (coding DNA reference sequence), crossing an exon/intron border

缺失范围跨越了外显子/内含子交接区

外显子/内含子交接区（不遵循3'规则）

NM_004006.1:c.1149del

when exon 10 ends with ..GAG and exon 11 starts with GGGT.. and the genomic DNA sequence shows that the last G-nucleotide of exon 10 is deleted (and not the G in exon 11), the deletion changing ..GAGGGGT.. to ..GAGGGT.. is described as c.1149del (not c.1152del, see exception in Numbering)

NOTE: it is allowed to describe the variant as NM_004006.1:c.1149delG

此时不遵循3'规则，不描述为c.1152del，而是c.1149delG

NM_004006.1:c.1152del

the deletion of the G nucleotide at the intron/exon border in the sequence CATGAGgt…/..agGGGTAC to CATGAGgt…/..agGG_TAC

NOTE: it is allowed to describe the variant as NM_004006.1:c.1152delG

NG_012232.1(NM_004006.1):c.1149+1del

the deletion of the G nucleotide at the exon/intron border in the sequence CATGAGgt…/..agGGGTAC to CATGAG_t…/..agGGGTAC (not c.1152del see Q&A)

NOTE: it is allowed to describe the variant as NG_012232.1(NM_004006.1):c.1149+1delG

NG_012232.1(NM_004006.1):c.4072-1234_5155-246del

a deletion of nucleotides c.4072-1234 to c.5155-246 removing exon 30 (starting at position c.4072) to exon 36 (ending at position c.5154) of the DMD-gene.

NOTE : c.4072-1234_5155-246delXXXXX, the size of the deletion (XXXXX) should not be described

断裂点位置详细：第一个断裂点在内含子29（4072上溯1234个核苷酸），第二个断裂点在内含子36（5155上溯246个核苷酸）

NG_012232.1(NM_004006.1):c.(4071+1_4072-1)_(5154+1_5155-1)del

a deletion of exon 30 (starting at position c.4072) to exon 36 (ending at position c.5154) of the DMD-gene. The deletion break point has not been sequenced. Exons 29 (ending at c.4071) and 37 (starting at nucleotide c.5155) have been tested an shown to be not deleted. The deletion therefore starts in intron 29 (position c.4071+1 to c.4072-1) and ends in intron 36 (position c.5154+1 to c.5155-1).

第一个断裂点在内含子29，第二个断裂点在内含子36，具体位置不详，所以给了一个完整内含子的范围

更多信息，关注公众号：何艺新筛手札