HGVS的變異格式


符號:

 

 

1.HGVS的變異格式由兩部分組成:

1.1 reference sequence file identifier (accession.version-number) :  actual description of a variant

比如:NG_012232.1(NM_004006.2):c.357+1G>A

NG_012232.1(NM_004006.2)是the reference sequence file identifier。

c.357+1G>A:the actual description of a variant

1.2 具體解釋

reference sequence file identifiter:只接受NCBI,EBI的公共文件的內容。包括NC_# (e.g. NC_000023.10), LRG_# (e.g. LRG_199), NG_# (e.g. NG_012232.1), ENSG00000182533.6, NM_# (e.g. NM_004006.2), ENST00000343849.2, NR_# (e.g. NR_002196.1) and NP_# (e.g. NP_003997.1)。注意,點號后面的內容是版本號,除了LRG_外,其它的格式都需要版本號。

actual description of a variant:由兩部分組成,一是參考序列的類型,二是具體的突變信息。

 

2.具體變異描述的內容(actual description of a variant)

2.1。參考序列的類型

2.2。具體的突變信息。

 2.2.1.蛋白

1.1替代:

   格式:“prefix”“amino_acid”“position”“new_amino_acid”

LRG_199p1:p.Trp24Cys missense 把一個氨基酸換成另一個氨基酸
LRG_199p1:p.Trp24Ter (p.Trp24*) nonsense 把一個氨基酸換成終止密碼子
NP_003997.1:p.Cys188= slient 氨基酸沒有變化

 

1.2缺失:

  格式:“prefix”“amino_acid(s)+position(s)_deleted”“del”

p.Ala3del 第三個氨基酸Ala缺失
p.Ala3_Ser5del  第三個氨基酸到第五個氨基酸缺失

 

1.3重復:

  格式:“prefix”“amino_acid(s)+position(s)_duplicated”“dup”

p.Ala3dup (one amino acid)a duplication of amino acid Ala3 in the sequence MetGlyAlaArgSerSerHis to MetGlyAlaAlaArgSerSerHis

 

1.4插入:

  格式:“prefix”“amino_acids+positions_flanking”“ins”“inserted_sequence”

p.His4_Gln5insAla :the insertion of amino acid Ala between amino acids His4 and Gln5 changing MetLysGlyHisGlnGlnCys to MetLysGlyHisAlaGlnGlnCys

 

1.5移碼(frame shift):移碼是插入或缺失的一種特例。

 格式: “prefix”“amino_acid”position”new_amino_acid”“fs”“Ter”“position_termination_site

p.Arg97ProfsTer23 :a variant with Arg97 as the first amino acid changed, shifting the reading frame, replacing it for a Pro and terminating at position Ter23

 解釋:第97位的Arg變為Pro,這次翻譯終止為從該位點數起的第23個氨基酸。

 

 2.2.2基因

在用coding DNA作為參考序列時,其有自己的坐標定義圖:

 

 2.1 替代 :

    格式: “prefix”“position_substituted”“reference_nucleotide””>”new_nucleotide”

 

    • NC_000023.10:g.33038255C>A
      a substitution of the C nucleotide at g.33038255 for an A
    • NG_012232.1(NM_004006.1):c.93+1G>T
      a substitution of the G nucleotide at c.93+1 (coding DNA reference sequence) with a T

2.2缺失

   格式:“prefix”“position(s)_deleted”“del”

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

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

 

2.3重復

  格式:“prefix”“position(s)_duplicated”“dup”

NM_004006.2:c.20_23dup (NC_000023.10:g.33229407_33229410dup)

a duplication from position c.20 to c.23 in the sequence AGAAGTAGAGG to AGAAGTAGATAGAGG

 

2.4插入:

   格式:“prefix”“positions_flanking”“ins”“inserted_sequence”

NC_000023.10:g.32862923_32862924insCCT (LRG_199t1:c.240_241insAGG)

the insertion of nucleotides CCT between nucleotides g.32862923 and g.32862924

 

2.5轉換:一段序列被參考基因組的另一段序列替換

  格式:“prefix”“positions_converted”“con”“positions_replacing_sequence”

NC_000022.10:g.42522624_42522669con42536337_42536382

conversion in exon 9 of the CYP2D6 gene replacing exon 9 nucleotides g.42522624 to g.42522669 with those of the 3’ flanking CYP2D7P1 gene, nucleotides g.42536337 to g.42536382 from the same genomic reference sequence (NC_000022.10)

 

2.6缺失插入

  格式:“prefix”“position(s)_deleted”“delins”“inserted_sequence”

g.6775delinsGA

a deletion of nucleotide g.6775 (a T, not described), replaced by nucleotides GA, changing ..AGGCTCATT.. to ..AGGCGACATT..

 

 參考文章:

http://varnomen.hgvs.org/recommendations/general/

http://www.sohu.com/a/158915410_603295


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