fa5b31d305066e1938953374d80b3782ef87e239 max Mon Sep 7 23:23:40 2026 -0700 Position box: accept a bare codon number, and a range of codon numbers "KAT6A p.495_533" used to land on codon 495 and silently drop the end of the range, and a bare codon number after a transcript accession was not understood at all, so "ENST00000265713.8 p.495" fell through the HGVS code and ended up on an unrelated locus. Nucleotide ranges already worked. The pseudo-HGVS layer now takes an optional _end on a bare codon number, and accepts a bare codon number or range after an NM_ or ENST accession as well as after a gene symbol, looking up the reference amino acids that HGVS wants and the user did not type. The accession forms require a literal "p", so "NM_006766.5 1483" keeps meaning what it meant. A hyphen is still not a range separator: c.1483-1599 is the HGVS intronic position and stays that way. Also fixes a read past the end of the protein sequence when the codon number was larger than the protein, and documents codon ranges in query.html. refs #38285 diff --git src/hg/htdocs/goldenPath/help/query.html src/hg/htdocs/goldenPath/help/query.html index 159b56eee34..81f19c8f843 100755 --- src/hg/htdocs/goldenPath/help/query.html +++ src/hg/htdocs/goldenPath/help/query.html @@ -29,30 +29,33 @@ Gene names
  • 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)
    • +
  • HGVS and accession searches on outdated RefSeq accession versions is available on hg38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

    @@ -73,30 +76,40 @@ VICC Gene Fusion Specification, e.g. TP53:e.5 or NM_000546:e.5. Optionally add an intronic offset: SYMBOL:e.N+offset navigates offset bases past the 3’ end of the exon (into the downstream intron), and SYMBOL:e.N-offset navigates offset bases before the 5’ start (into the upstream intron). Useful for splice site inspection: BRCA2:e.10+2 lands 2 bp into the intron after exon 10.

    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.

    +

    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. @@ -171,30 +184,40 @@ + + +
    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
    3:1-1000000Compact exon notation from the 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.
    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    		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