0f23d17640ca30e2c9ee456c7e15966cabd3bc57 max Mon Sep 7 23:32:24 2026 -0700 Position box: let a hyphen separate a range of codons, e.g. "BRCA1 100-200" A bare number after a gene symbol has always meant a codon, and "KAT6A 495-533" was already accepted -- it just landed on codon 495 and dropped the rest, the same silent truncation that the underscore form had. A hyphen now separates a range wherever the coordinates are protein: after a gene symbol with no prefix, and after an explicit p. with a symbol or a transcript accession. The hyphen stays out of c. and n. terms, where HGVS already uses it for an intron offset. KAT6A c.1483-1599 is still the single base 1599 nt before c.1483, not codons 1483 to 1599, and there are now regression tests pinning both readings so the two do not drift into each other. refs #38285 diff --git src/hg/htdocs/goldenPath/help/query.html src/hg/htdocs/goldenPath/help/query.html index 81f19c8f843..3a587371c96 100755 --- src/hg/htdocs/goldenPath/help/query.html +++ src/hg/htdocs/goldenPath/help/query.html @@ -30,31 +30,31 @@
  • Accession numbers
  • An mRNA, EST or STS marker
  • Keywords from the GenBank description of an mRNA
  • HGVS terms
  • gnomAD variant IDs
  • Exon positions: SYMBOL exon N or SYMBOL:e.N[+/-offset] (e.g. TP53 exon 5, BRCA2:e.10, NM_000546:e.5+2)
  • Codon or nucleotide positions and ranges, with or without the amino acid letters - (e.g. BRAF p.600, KAT6A p.495_533, KAT6A c.1483_1599)
    • + (e.g. BRAF 600, KAT6A 495-533, KAT6A c.1483_1599)
  • HGVS and accession searches on outdated RefSeq accession versions is available on hg38

    • To specify a genome position:

    1. Select the desired clade, genome and assembly
    2. Enter the desired query in the "Position/Search Term" box (see sample queries below)
    3. Click the "Go" button
    @@ -82,33 +82,40 @@

    Exon numbering is 1-based and follows transcript order (exon 1 is the 5′ exon). Genes are looked up in order: MANE, GENCODE/UCSC (knownGene), all RefSeq, then historical RefSeq. To jump to a codon instead, just enter it after the gene, e.g. BRAF 600, use the HGVS notation (see below), or right-click any transcript in the browser and select “Zoom to codon”.

    A codon or nucleotide number can also be given as a range, which is often what you want when a paper describes a variant or a domain that covers more than one codon. Write the two numbers with an underscore between them, as HGVS does: KAT6A p.495_533 or KAT6A c.1483_1599. The amino acid letters are optional, so KAT6A p.Lys495_Ser533 works as well, and an Ensembl or RefSeq transcript can stand in -for the gene symbol, e.g. ENST00000265713.8 p.495_533. A hyphen does not mean a range: -in HGVS, c.1483-1599 is a position in the intron 1599 bases before -c.1483, and the Browser reads it that way.

    +for the gene symbol, e.g. ENST00000265713.8 p.495_533.

    + +

    +For codons you can use a hyphen instead of the underscore, so BRCA1 100-200 and +KAT6A p.495-533 both work. This shortcut is for codons only. After +c. or n. a hyphen keeps its HGVS meaning, which is an intron offset +rather than a range: KAT6A c.1483-1599 is the single base 1599 bases before +c.1483, deep in the preceding intron, and the Browser takes you there. So +KAT6A 100-200 is a stretch of 101 codons, while KAT6A c.100-200 is one +base. If you mean a range of nucleotides, always use the underscore.

    Sample queries

    Below is a list of examples that might be used to query the Genome Browser. Note that not every query listed here will produce a result in every assembly. The list serves only to illustrate the different types of queries that can be performed. @@ -185,39 +192,40 @@ VICC Gene Fusion Specification. Jumps to exon 5 of TP53, or to 2 bp past the end / 3 bp before the start of BRCA2 exon 10 (useful for splice site inspection). The +N/-N offset is optional. - + + letters are optional, a bare number after a gene symbol is read as a codon, and the gene symbol + can be replaced by a RefSeq or Ensembl transcript. Ranges of codons take either an underscore + or a hyphen; ranges of nucleotides take only the underscore, because after c. or + n. a hyphen is an HGVS intron offset, so c.1483-1599 means the single + base 1599 bases before c.1483. A gene symbol with more than one transcript + brings up a disambiguation page.
    QueryGenome Browser Response
    chr7 Displays all of chromosome 7
    chr3:1-1000000 Displays the first million bases of chromosome 3, counting from the p-arm telomere
    NM_000310.4(PPT1):c.271_287del17insTT
    NM_007262.5(PARK7):c.-24+75_-24+92dup
    NM_006172.4(NPPA):c.456_*1delAA
    MYH11:c.503-14_503-12del
    NM_198576.4(AGRN):c.1057C>T
    NM_198056.3:c.1654G>T
    NP_002993.1:p.Asp92Glu
    NP_002993.1:p.D92E
    BRCA1 Ala744Cys
    BRCA1 A744C
    LRG_100t1:c.4G>A
    LRG_100t1:n.1
    LRG_456p1:p.Ser190Leu
    LRG_321:g.16409_16461del
    ENST00000002596.6:c.-108-6848A>G
    ENSP00000005178.5:p.Val20Gly
    chrX:g.31500000_31600000del
    NR_111987:n.-1
    NM_015102.5:n.3038-2
    NM_001372044:c.1528_1530del    		 Displays the region that matches the HGVS expression, usually in the format <transcript or protein>:<position> <amino acid or nucleotide change>
    If a gene symbol is used, HGVS search will try all RefSeq transcripts to find the nucleotide or amino acid at the position indicated in the expression. If there are multiple matches, a disambiguation page will be shown. If the RefSeq sequence differs from the genome sequence, then currently the search will use the genome, not the transcript, for codon counting and amino acid / nucleotide comparison. Please contact us if this is inconvenient.
    KAT6A p.495
    KAT6A p.495_533
    KAT6A p.Lys495_Ser533
    - ENST00000265713.8 p.495_533
    NM_006766.5 p.495
    KAT6A c.1483
    - KAT6A c.1483_1599
    ENST00000265713.8 c.1483_1599    		KAT6A p.495
    KAT6A 495
    KAT6A p.495_533
    KAT6A 495-533
    + KAT6A p.Lys495_Ser533
    ENST00000265713.8 p.495_533
    NM_006766.5 p.495
    + KAT6A c.1483
    KAT6A c.1483_1599
    ENST00000265713.8 c.1483_1599    		 A codon or nucleotide position, or a range of them, with no sequence change. The amino acid - letters are optional and the gene symbol can be replaced by a RefSeq or Ensembl transcript. - Note that the range separator is the underscore, as in HGVS; a hyphen means something else, so - c.1483-1599 is read as a position in the intron 1599 bases before - c.1483. A gene symbol with more than one transcript brings up a disambiguation - page.
    NM_198056.2:c.1A>C An example of an HGVS search on a previous NM version that is now outdated. Support for previous NM accessions is only available on hg38.
    1-55051215-G-GA Displays the region that matches the gnomAD variant ID, 1-55051215-G-GA