Search by Genic region
Multiple Alignments (by aa haplotype frequency)
Multiple Alignments (by aa haplotype similarity)
| geneid | 442862 |
|---|---|
| ensemblid | ENSG00000169807.10 |
| hgncid | 21504 |
| symbol | PRY2 |
| name | PTPN13 like Y-linked 2 |
| refseq_nuc | NM_001002758.1 |
| refseq_prot | NP_001002758.1 |
| ensembl_nuc | ENST00000303804.5 |
| ensembl_prot | ENSP00000303300.1 |
| mane_status | MANE Select |
| chr | chrY |
| start | 22071756 |
| end | 22096007 |
| strand | - |
| ver | v1.2 |
| region | chrY:22071756-22096007 |
| region5000 | chrY:22066756-22101007 |
| regionname0 | PRY2_chrY_22071756_22096007 |
| regionname5000 | PRY2_chrY_22066756_22101007 |
| ahapid | grch38/chm13v2 1/0: The haplotype type is the same as GRCh380/1: The haplotype type is the same as CHM13v20/0: The haplotype type matches neither GRCh38 nor CHM13v21/1: The haplotype type is the same on both GRCh38 and CHM13v2
|
alen | total | AFR | AMR | EAS | EUR | SAS | JPT | regionname | genename | aa | chr | start | end |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| a0001 | 0/0 | 147 | 4 | 0 | 0 | 4 | 0 | 0 | 4 | PRY2_chrY_22066756_22101007 | PRY2 | copy fasta | chrY | 22066756 | 22101007 |
| chapid | grch38/chm13v2 1/0: The haplotype type is the same as GRCh380/1: The haplotype type is the same as CHM13v20/0: The haplotype type matches neither GRCh38 nor CHM13v21/1: The haplotype type is the same on both GRCh38 and CHM13v2
|
clen | total | AFR | AMR | EAS | EUR | SAS | regionname | genename | cseq | chr | start | end |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| c0001 | 0/0 | 444 | 4 | 0 | 0 | 4 | 0 | 0 | PRY2_chrY_22066756_22101007 | PRY2 | copy fasta | chrY | 22066756 | 22101007 |
| thapid | grch38chm13v2 1/0: The haplotype type is the same as GRCh380/1: The haplotype type is the same as CHM13v20/0: The haplotype type matches neither GRCh38 nor CHM13v21/1: The haplotype type is the same on both GRCh38 and CHM13v2
|
tlen | total | AFR | AMR | EAS | EUR | SAS | regionname | genename | tseq | chr | start | end |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| t0001 | 0/0 | 795 | 3 | 0 | 0 | 3 | 0 | 0 | PRY2_chrY_22066756_22101007 | PRY2 | copy fasta | chrY | 22066756 | 22101007 |
| t0002 | 0/0 | 795 | 1 | 0 | 0 | 1 | 0 | 0 | PRY2_chrY_22066756_22101007 | PRY2 | copy fasta | chrY | 22066756 | 22101007 |
| ghapid | grch38/chm13v2 1/0: The haplotype type is the same as GRCh380/1: The haplotype type is the same as CHM13v20/0: The haplotype type matches neither GRCh38 nor CHM13v21/1: The haplotype type is the same on both GRCh38 and CHM13v2
|
total | AFR | AMR | EAS | EUR | SAS | regionname | genename | chr | start | end |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| g0001 | 0/0 | 1 | 0 | 0 | 1 | 0 | 0 | PRY2_chrY_22066756_22101007 | PRY2 | chrY | 22066756 | 22101007 |
| g0002 | 0/0 | 1 | 0 | 0 | 1 | 0 | 0 | PRY2_chrY_22066756_22101007 | PRY2 | chrY | 22066756 | 22101007 |
| g0003 | 0/0 | 1 | 0 | 0 | 1 | 0 | 0 | PRY2_chrY_22066756_22101007 | PRY2 | chrY | 22066756 | 22101007 |
| g0004 | 0/0 | 1 | 0 | 0 | 1 | 0 | 0 | PRY2_chrY_22066756_22101007 | PRY2 | chrY | 22066756 | 22101007 |
| achapid | grch38/chm13v2 1/0: The haplotype type is the same as GRCh380/1: The haplotype type is the same as CHM13v20/0: The haplotype type matches neither GRCh38 nor CHM13v21/1: The haplotype type is the same on both GRCh38 and CHM13v2
|
clen | total | AFR | AMR | EAS | EUR | SAS | regionname | genename | cseq | chr | start | end |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| a0001c0001 | 0/0 | 444 | 4 | 0 | 0 | 4 | 0 | 0 | PRY2_chrY_22066756_22101007 | PRY2 | copy fasta | chrY | 22066756 | 22101007 |
| acthapid | grch38chm13v2 | tlen | total | AFR | AMR | EAS | EUR | SAS | regionname | genename | tseq | chr | start | end |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| a0001c0001t0001 | 0/0 | 1238 | 3 | 0 | 0 | 3 | 0 | 0 | PRY2_chrY_22066756_22101007 | PRY2 | copy fasta | chrY | 22066756 | 22101007 |
| a0001c0001t0002 | 0/0 | 1238 | 1 | 0 | 0 | 1 | 0 | 0 | PRY2_chrY_22066756_22101007 | PRY2 | copy fasta | chrY | 22066756 | 22101007 |
| actghapid | grch38/chm13v2 1/0: The haplotype type is the same as GRCh380/1: The haplotype type is the same as CHM13v20/0: The haplotype type matches neither GRCh38 nor CHM13v21/1: The haplotype type is the same on both GRCh38 and CHM13v2
|
total | AFR | AMR | EAS | EUR | SAS | regionname | genename | chr | start | end |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| a0001c0001t0001g0002 | 0/0 | 1 | 0 | 0 | 1 | 0 | 0 | PRY2_chrY_22066756_22101007 | PRY2 | chrY | 22066756 | 22101007 |
| a0001c0001t0001g0003 | 0/0 | 1 | 0 | 0 | 1 | 0 | 0 | PRY2_chrY_22066756_22101007 | PRY2 | chrY | 22066756 | 22101007 |
| a0001c0001t0001g0004 | 0/0 | 1 | 0 | 0 | 1 | 0 | 0 | PRY2_chrY_22066756_22101007 | PRY2 | chrY | 22066756 | 22101007 |
| a0001c0001t0002g0001 | 0/0 | 1 | 0 | 0 | 1 | 0 | 0 | PRY2_chrY_22066756_22101007 | PRY2 | chrY | 22066756 | 22101007 |
| sampleid | ID haplotypeid
|
ahapid | chapid | thapid | ghapid | gpopname | popname | regionname | genename | chr | start | end |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| NA18974 | hp1 | a0001 | c0001 | t0001 | g0004 | EAS | JPT | PRY2_chrY_22066756_22101007 | PRY2 | chrY | 22066756 | 22101007 |
| NA18983 | hp1 | a0001 | c0001 | t0001 | g0002 | EAS | JPT | PRY2_chrY_22066756_22101007 | PRY2 | chrY | 22066756 | 22101007 |
| NA18985 | hp1 | a0001 | c0001 | t0002 | g0001 | EAS | JPT | PRY2_chrY_22066756_22101007 | PRY2 | chrY | 22066756 | 22101007 |
| NA19089 | hp1 | a0001 | c0001 | t0001 | g0003 | EAS | JPT | PRY2_chrY_22066756_22101007 | PRY2 | chrY | 22066756 | 22101007 |
| chr:pos | ref | alt | # # of ahapid:amino-acid(protein) level |
ahapids | # # of haplotypeids |
haplotypeids | annotation | impact | hgvs_c | hgvs_p | genename | geneid | featuretype | featureid | transcript_biotype | rank | cdna cdna pos length |
cds cds pos length |
aa aa pos length |
distance | status | chr | pos |
|---|
| chr:pos | ref | alt | # # of chapid |
chapids | # # of haplotypeids |
haplotypeids | annotation | impact | hgvs_c | hgvs_p | genename | geneid | featuretype | featureid | transcript_biotype | rank | cdna cdna pos length |
cds cds pos length |
aa aa pos length |
distance | status | chr | pos |
|---|
| chr:pos | ref | alt | # # of thapid:transcript level |
thapids | # # of haplotypeids |
haplotypeids | annotation | impact | hgvs_c | hgvs_p | genename | geneid | featuretype | featureid | transcript_biotype | rank | cdna cdna pos length |
cds cds pos length |
aa aa pos length |
distance | status | chr | pos |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| chrY:22071856
|
C | T | 1 | a0001c0001t0002 | 1 | NA18985.hp1 | 3_prime_UTR_variant | MODIFIER | c.*467G>A | PRY2 | ENSG00000169807.10 | transcript | ENST00000303804.5 | protein_coding | 5/5 | 467 | chrY | 22071856 |
| chr:pos | ref | alt | # # of ghapid:genebody level |
ghapids | # # of haplotypeids |
haplotypeids | annotation | impact | hgvs_c | hgvs_p | genename | geneid | featuretype | featureid | genebody_biotype | rank | cdna cdna pos length |
cds cds pos length |
aa aa pos length |
distance | status | chr | pos |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| chrY:22077301
|
A | G | 2 | a0001c0001t0001g0002a0001c0001t0001g0003 | 2 | NA18983.hp1 NA19089.hp1 |
intron_variant | MODIFIER | c.186-4720T>C | PRY2 | ENSG00000169807.10 | transcript | ENST00000303804.5 | protein_coding | 4/4 | chrY | 22077301 | ||||||
| chrY:22078040
|
CA | C | 1 | a0001c0001t0001g0003 | 1 | NA19089.hp1 | intron_variant | MODIFIER | c.185+4039delT | PRY2 | ENSG00000169807.10 | transcript | ENST00000303804.5 | protein_coding | 4/4 | chrY | 22078040 | ||||||
| chrY:22078688
|
T | TC | 1 | a0001c0001t0001g0003 | 1 | NA19089.hp1 | intron_variant | MODIFIER | c.185+3391dupG | PRY2 | ENSG00000169807.10 | transcript | ENST00000303804.5 | protein_coding | 4/4 | chrY | 22078688 | ||||||
| chrY:22079212
|
C | CAT | 1 | a0001c0001t0001g0003 | 1 | NA19089.hp1 | intron_variant | MODIFIER | c.185+2866_185+2867d others(4): Show |
PRY2 | ENSG00000169807.10 | transcript | ENST00000303804.5 | protein_coding | 4/4 | chrY | 22079212 | ||||||
| chrY:22079266
|
A | G | 1 | a0001c0001t0001g0003 | 1 | NA19089.hp1 | intron_variant | MODIFIER | c.185+2814T>C | PRY2 | ENSG00000169807.10 | transcript | ENST00000303804.5 | protein_coding | 4/4 | chrY | 22079266 | ||||||
| chrY:22079297
|
TC | T | 1 | a0001c0001t0001g0003 | 1 | NA19089.hp1 | intron_variant | MODIFIER | c.185+2782delG | PRY2 | ENSG00000169807.10 | transcript | ENST00000303804.5 | protein_coding | 4/4 | chrY | 22079297 | ||||||
| chrY:22079301
|
TC | T | 1 | a0001c0001t0001g0003 | 1 | NA19089.hp1 | intron_variant | MODIFIER | c.185+2778delG | PRY2 | ENSG00000169807.10 | transcript | ENST00000303804.5 | protein_coding | 4/4 | chrY | 22079301 | ||||||
| chrY:22080158
|
A | AG | 1 | a0001c0001t0001g0003 | 1 | NA19089.hp1 | intron_variant | MODIFIER | c.185+1921dupC | PRY2 | ENSG00000169807.10 | transcript | ENST00000303804.5 | protein_coding | 4/4 | chrY | 22080158 | ||||||
| chrY:22080658
|
C | T | 1 | a0001c0001t0001g0002 | 1 | NA18983.hp1 | intron_variant | MODIFIER | c.185+1422G>A | PRY2 | ENSG00000169807.10 | transcript | ENST00000303804.5 | protein_coding | 4/4 | chrY | 22080658 | ||||||
| chrY:22081086
|
C | T | 3 | a0001c0001t0001g0002a0001c0001t0001g0003a0001c0001t0001g0004 | 3 | NA18974.hp1 NA18983.hp1 NA19089.hp1 |
intron_variant | MODIFIER | c.185+994G>A | PRY2 | ENSG00000169807.10 | transcript | ENST00000303804.5 | protein_coding | 4/4 | chrY | 22081086 | ||||||
| chrY:22081165
|
C | T | 2 | a0001c0001t0001g0002a0001c0001t0001g0003 | 2 | NA18983.hp1 NA19089.hp1 |
intron_variant | MODIFIER | c.185+915G>A | PRY2 | ENSG00000169807.10 | transcript | ENST00000303804.5 | protein_coding | 4/4 | chrY | 22081165 | ||||||
| chrY:22081292
|
A | G | 1 | a0001c0001t0001g0004 | 1 | NA18974.hp1 | intron_variant | MODIFIER | c.185+788T>C | PRY2 | ENSG00000169807.10 | transcript | ENST00000303804.5 | protein_coding | 4/4 | chrY | 22081292 | ||||||
| chrY:22081345
|
T | C | 1 | a0001c0001t0001g0004 | 1 | NA18974.hp1 | intron_variant | MODIFIER | c.185+735A>G | PRY2 | ENSG00000169807.10 | transcript | ENST00000303804.5 | protein_coding | 4/4 | chrY | 22081345 | ||||||
| chrY:22085946
|
C | CA | 2 | a0001c0001t0001g0004a0001c0001t0002g0001 | 2 | NA18974.hp1 NA18985.hp1 |
intron_variant | MODIFIER | c.-52-1056dupT | PRY2 | ENSG00000169807.10 | transcript | ENST00000303804.5 | protein_coding | 2/4 | chrY | 22085946 | ||||||
| chrY:22088119
|
A | G | 1 | a0001c0001t0001g0004 | 1 | NA18974.hp1 | intron_variant | MODIFIER | c.-52-3228T>C | PRY2 | ENSG00000169807.10 | transcript | ENST00000303804.5 | protein_coding | 2/4 | chrY | 22088119 | ||||||
| chrY:22089240
|
G | GT | 1 | a0001c0001t0002g0001 | 1 | NA18985.hp1 | intron_variant | MODIFIER | c.-52-4350dupA | PRY2 | ENSG00000169807.10 | transcript | ENST00000303804.5 | protein_coding | 2/4 | chrY | 22089240 | ||||||
| chrY:22089240
|
GT | G | 1 | a0001c0001t0001g0004 | 1 | NA18974.hp1 | intron_variant | MODIFIER | c.-52-4350delA | PRY2 | ENSG00000169807.10 | transcript | ENST00000303804.5 | protein_coding | 2/4 | chrY | 22089240 | ||||||
| chrY:22089569
|
C | CA | 1 | a0001c0001t0001g0004 | 1 | NA18974.hp1 | intron_variant | MODIFIER | c.-52-4679dupT | PRY2 | ENSG00000169807.10 | transcript | ENST00000303804.5 | protein_coding | 2/4 | chrY | 22089569 | ||||||
| chrY:22089626
|
A | AG | 1 | a0001c0001t0001g0004 | 1 | NA18974.hp1 | intron_variant | MODIFIER | c.-52-4736dupC | PRY2 | ENSG00000169807.10 | transcript | ENST00000303804.5 | protein_coding | 2/4 | chrY | 22089626 | ||||||
| chrY:22090293
|
G | GA | 1 | a0001c0001t0001g0004 | 1 | NA18974.hp1 | intron_variant | MODIFIER | c.-52-5403dupT | PRY2 | ENSG00000169807.10 | transcript | ENST00000303804.5 | protein_coding | 2/4 | chrY | 22090293 | ||||||
| chrY:22090305
|
T | TC | 1 | a0001c0001t0001g0004 | 1 | NA18974.hp1 | intron_variant | MODIFIER | c.-52-5415dupG | PRY2 | ENSG00000169807.10 | transcript | ENST00000303804.5 | protein_coding | 2/4 | chrY | 22090305 | ||||||
| chrY:22090688
|
G | GA | 1 | a0001c0001t0001g0004 | 1 | NA18974.hp1 | intron_variant | MODIFIER | c.-53+5043dupT | PRY2 | ENSG00000169807.10 | transcript | ENST00000303804.5 | protein_coding | 2/4 | chrY | 22090688 | ||||||
| chrY:22090760
|
G | GA | 1 | a0001c0001t0001g0004 | 1 | NA18974.hp1 | intron_variant | MODIFIER | c.-53+4971dupT | PRY2 | ENSG00000169807.10 | transcript | ENST00000303804.5 | protein_coding | 2/4 | chrY | 22090760 | ||||||
| chrY:22091084
|
T | TA | 1 | a0001c0001t0001g0004 | 1 | NA18974.hp1 | intron_variant | MODIFIER | c.-53+4647dupT | PRY2 | ENSG00000169807.10 | transcript | ENST00000303804.5 | protein_coding | 2/4 | chrY | 22091084 | ||||||
| chrY:22091092
|
T | TA | 1 | a0001c0001t0001g0004 | 1 | NA18974.hp1 | intron_variant | MODIFIER | c.-53+4639dupT | PRY2 | ENSG00000169807.10 | transcript | ENST00000303804.5 | protein_coding | 2/4 | chrY | 22091092 | ||||||
| chrY:22091312
|
A | T | 3 | a0001c0001t0001g0002a0001c0001t0001g0004a0001c0001t0002g0001 | 3 | NA18974.hp1 NA18983.hp1 NA18985.hp1 |
intron_variant | MODIFIER | c.-53+4420T>A | PRY2 | ENSG00000169807.10 | transcript | ENST00000303804.5 | protein_coding | 2/4 | chrY | 22091312 | ||||||
| chrY:22091356
|
T | TAAAA | 1 | a0001c0001t0001g0004 | 1 | NA18974.hp1 | intron_variant | MODIFIER | c.-53+4372_-53+4375d others(6): Show |
PRY2 | ENSG00000169807.10 | transcript | ENST00000303804.5 | protein_coding | 2/4 | chrY | 22091356 | ||||||
| chrY:22091536
|
T | TA | 1 | a0001c0001t0001g0004 | 1 | NA18974.hp1 | intron_variant | MODIFIER | c.-53+4195dupT | PRY2 | ENSG00000169807.10 | transcript | ENST00000303804.5 | protein_coding | 2/4 | chrY | 22091536 | ||||||
| chrY:22091874
|
T | TA | 1 | a0001c0001t0001g0004 | 1 | NA18974.hp1 | intron_variant | MODIFIER | c.-53+3857dupT | PRY2 | ENSG00000169807.10 | transcript | ENST00000303804.5 | protein_coding | 2/4 | chrY | 22091874 | ||||||
| chrY:22091956
|
T | TG | 1 | a0001c0001t0001g0004 | 1 | NA18974.hp1 | intron_variant | MODIFIER | c.-53+3775dupC | PRY2 | ENSG00000169807.10 | transcript | ENST00000303804.5 | protein_coding | 2/4 | chrY | 22091956 | ||||||
| chrY:22092479
|
A | AT | 1 | a0001c0001t0001g0004 | 1 | NA18974.hp1 | intron_variant | MODIFIER | c.-53+3252dupA | PRY2 | ENSG00000169807.10 | transcript | ENST00000303804.5 | protein_coding | 2/4 | chrY | 22092479 | ||||||
| chrY:22093297
|
A | AG | 1 | a0001c0001t0001g0004 | 1 | NA18974.hp1 | intron_variant | MODIFIER | c.-53+2434dupC | PRY2 | ENSG00000169807.10 | transcript | ENST00000303804.5 | protein_coding | 2/4 | chrY | 22093297 | ||||||
| chrY:22093570
|
C | CA | 1 | a0001c0001t0001g0004 | 1 | NA18974.hp1 | intron_variant | MODIFIER | c.-53+2161dupT | PRY2 | ENSG00000169807.10 | transcript | ENST00000303804.5 | protein_coding | 2/4 | chrY | 22093570 | ||||||
| chrY:22093596
|
G | GT | 1 | a0001c0001t0001g0004 | 1 | NA18974.hp1 | intron_variant | MODIFIER | c.-53+2135dupA | PRY2 | ENSG00000169807.10 | transcript | ENST00000303804.5 | protein_coding | 2/4 | chrY | 22093596 | ||||||
| chrY:22093681
|
G | GA | 1 | a0001c0001t0001g0004 | 1 | NA18974.hp1 | intron_variant | MODIFIER | c.-53+2050dupT | PRY2 | ENSG00000169807.10 | transcript | ENST00000303804.5 | protein_coding | 2/4 | chrY | 22093681 | ||||||
| chrY:22094023
|
G | GA | 1 | a0001c0001t0001g0004 | 1 | NA18974.hp1 | intron_variant | MODIFIER | c.-53+1708dupT | PRY2 | ENSG00000169807.10 | transcript | ENST00000303804.5 | protein_coding | 2/4 | chrY | 22094023 | ||||||
| chrY:22094521
|
A | ATT | 1 | a0001c0001t0001g0004 | 1 | NA18974.hp1 | intron_variant | MODIFIER | c.-53+1209_-53+1210d others(4): Show |
PRY2 | ENSG00000169807.10 | transcript | ENST00000303804.5 | protein_coding | 2/4 | chrY | 22094521 | ||||||
| chrY:22094649
|
G | GC | 1 | a0001c0001t0001g0004 | 1 | NA18974.hp1 | intron_variant | MODIFIER | c.-53+1082dupG | PRY2 | ENSG00000169807.10 | transcript | ENST00000303804.5 | protein_coding | 2/4 | chrY | 22094649 | ||||||
| chrY:22094827
|
C | CT | 1 | a0001c0001t0001g0004 | 1 | NA18974.hp1 | intron_variant | MODIFIER | c.-53+904dupA | PRY2 | ENSG00000169807.10 | transcript | ENST00000303804.5 | protein_coding | 2/4 | chrY | 22094827 | ||||||
| chrY:22095052
|
G | GTC | 1 | a0001c0001t0001g0004 | 1 | NA18974.hp1 | intron_variant | MODIFIER | c.-53+678_-53+679dup others(2): Show |
PRY2 | ENSG00000169807.10 | transcript | ENST00000303804.5 | protein_coding | 2/4 | chrY | 22095052 | ||||||
| chrY:22095137
|
T | TA | 1 | a0001c0001t0001g0004 | 1 | NA18974.hp1 | intron_variant | MODIFIER | c.-53+594dupT | PRY2 | ENSG00000169807.10 | transcript | ENST00000303804.5 | protein_coding | 2/4 | chrY | 22095137 | ||||||
| chrY:22095580
|
A | AG | 4 | a0001c0001t0001g0002a0001c0001t0001g0003a0001c0001t0001g0004others(1): Show | 4 | NA18974.hp1 NA18983.hp1 NA18985.hp1 others(1): Show |
intron_variant | MODIFIER | c.-53+151dupC | PRY2 | ENSG00000169807.10 | transcript | ENST00000303804.5 | protein_coding | 2/4 | chrY | 22095580 |