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