SNP Links for Gene (Select 132158) - SNP

Variant type:: SNV
Alleles:: T>C [Show Flanks]
Chromosome:: 3:52285975 (GRCh38)
3:52319991 (GRCh37)
Canonical SPDI:: NC_000003.12:52285974:T:C
Gene:: GLYCTK (Varview), LOC107986086 (Varview)
Functional Consequence:: intron_variant,upstream_transcript_variant,2KB_upstream_variant
Validated:: by frequency,by alfa,by cluster
MAF:: C=0./0 (ALFA)
C=0.000004/1 (TOPMED)
C=0.000007/1 (GnomAD)
HGVS:: NC_000003.12:g.52285975T>C, NC_000003.11:g.52319991T>C, NG_023246.1:g.3156T>C

Select item 14901618606.

rs1490161860 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A [Show Flanks]
Chromosome:: 3:52292744 (GRCh38)
3:52326760 (GRCh37)
Canonical SPDI:: NC_000003.12:52292743:G:A
Gene:: GLYCTK (Varview)
Functional Consequence:: coding_sequence_variant,intron_variant,3_prime_UTR_variant,non_coding_transcript_variant,stop_gained
Validated:: by frequency,by alfa
MAF:: A=0.000071/1 (ALFA)
A=0.000004/1 (TOPMED)
HGVS:: NC_000003.12:g.52292744G>A, NC_000003.11:g.52326760G>A, NG_023246.1:g.9925G>A, NM_145262.4:c.1190G>A, NM_145262.3:c.1190G>A, NR_026699.2:n.1280G>A, NR_026699.1:n.1288G>A, NR_026701.2:n.1278G>A, NR_026701.1:n.1286G>A, NM_001144951.2:c.*309G>A, NM_001144951.1:c.*309G>A, XM_024453351.2:c.1190G>A, XM_024453351.1:c.1190G>A, XM_024453352.2:c.*309G>A, XM_024453352.1:c.*309G>A, XM_017005730.2:c.809G>A, XM_017005730.1:c.809G>A, NP_660305.2:p.Trp397Ter, XP_024309119.1:p.Trp397Ter, XP_016861219.1:p.Trp270Ter

Select item 14901516857.

rs1490151685 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A,C [Show Flanks]
Chromosome:: 3:52295180 (GRCh38)
3:52329196 (GRCh37)
Canonical SPDI:: NC_000003.12:52295179:G:A,NC_000003.12:52295179:G:C
Gene:: GLYCTK (Varview), MIR135A1 (Varview)
Functional Consequence:: 2KB_upstream_variant,upstream_transcript_variant,genic_downstream_transcript_variant,3_prime_UTR_variant,non_coding_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: C=0.00008/1 (ALFA)
HGVS:: NC_000003.12:g.52295180G>A, NC_000003.12:g.52295180G>C, NC_000003.11:g.52329196G>A, NC_000003.11:g.52329196G>C, NG_023246.1:g.12361G>A, NG_023246.1:g.12361G>C, NM_145262.4:c.*2054G>A, NM_145262.4:c.*2054G>C, NM_145262.3:c.*2054G>A, NM_145262.3:c.*2054G>C, NR_026699.2:n.3716G>A, NR_026699.2:n.3716G>C, NR_026699.1:n.3724G>A, NR_026699.1:n.3724G>C, NR_026701.2:n.3600G>A, NR_026701.2:n.3600G>C, NR_026701.1:n.3608G>A, NR_026701.1:n.3608G>C, NM_001144951.2:c.*2745G>A, NM_001144951.2:c.*2745G>C, NR_026700.2:n.2708G>A, NR_026700.2:n.2708G>C, NR_026700.1:n.2716G>A, NR_026700.1:n.2716G>C, NR_026702.2:n.2638G>A, NR_026702.2:n.2638G>C, NR_026702.1:n.2646G>A, NR_026702.1:n.2646G>C, XM_024453351.2:c.*2054G>A, XM_024453351.2:c.*2054G>C, XM_024453352.2:c.*2745G>A, XM_024453352.2:c.*2745G>C, XM_017005730.2:c.*2054G>A, XM_017005730.2:c.*2054G>C

Select item 14900543538.

rs1490054353 [Homo sapiens]

Variant type:: SNV
Alleles:: A>G [Show Flanks]
Chromosome:: 3:52293680 (GRCh38)
3:52327696 (GRCh37)
Canonical SPDI:: NC_000003.12:52293679:A:G
Gene:: GLYCTK (Varview)
Functional Consequence:: downstream_transcript_variant,non_coding_transcript_variant,3_prime_UTR_variant,genic_downstream_transcript_variant
Validated:: by frequency,by alfa
MAF:: G=0./0 (ALFA)
G=0.000007/1 (GnomAD)
HGVS:: NC_000003.12:g.52293680A>G, NC_000003.11:g.52327696A>G, NG_023246.1:g.10861A>G, NM_145262.4:c.*554A>G, NM_145262.3:c.*554A>G, NR_026699.2:n.2216A>G, NR_026699.1:n.2224A>G, NR_026701.2:n.2100A>G, NR_026701.1:n.2108A>G, NM_001144951.2:c.*1245A>G, NR_026700.2:n.1208A>G, NR_026700.1:n.1216A>G, NR_026702.2:n.1138A>G, NR_026702.1:n.1146A>G, XM_024453351.2:c.*554A>G, XM_024453352.2:c.*1245A>G, XM_017005730.2:c.*554A>G

Select item 14900004609.

rs1490000460 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A [Show Flanks]
Chromosome:: 3:52285983 (GRCh38)
3:52319999 (GRCh37)
Canonical SPDI:: NC_000003.12:52285982:G:A
Gene:: GLYCTK (Varview), LOC107986086 (Varview)
Functional Consequence:: intron_variant,upstream_transcript_variant,2KB_upstream_variant
Validated:: by frequency
MAF:: A=0.000007/1 (GnomAD)
HGVS:: NC_000003.12:g.52285983G>A, NC_000003.11:g.52319999G>A, NG_023246.1:g.3164G>A

Select item 148994456510.

rs1489944565 [Homo sapiens]

Variant type:: DELINS
Alleles:: ->TCA [Show Flanks]
Chromosome:: 3:52291180 (GRCh38)
3:52325197 (GRCh37)
Canonical SPDI:: NC_000003.12:52291180:ATCA:ATCATCA
Gene:: GLYCTK (Varview), GLYCTK-AS1 (Varview)
Functional Consequence:: intron_variant,upstream_transcript_variant,2KB_upstream_variant
Validated:: by frequency,by alfa
MAF:: ATCATCA=0.000071/1 (ALFA)
ATC=0.000004/1 (TOPMED)
HGVS:: NC_000003.12:g.52291182_52291184dup, NC_000003.11:g.52325198_52325200dup, NG_023246.1:g.8363_8365dup

Select item 148981223611.

rs1489812236 [Homo sapiens]

Variant type:: SNV
Alleles:: C>T [Show Flanks]
Chromosome:: 3:52293083 (GRCh38)
3:52327099 (GRCh37)
Canonical SPDI:: NC_000003.12:52293082:C:T
Gene:: GLYCTK (Varview)
Functional Consequence:: coding_sequence_variant,synonymous_variant,missense_variant,3_prime_UTR_variant,non_coding_transcript_variant
Validated:: by frequency
MAF:: T=0.000008/2 (GnomAD_exomes)
HGVS:: NC_000003.12:g.52293083C>T, NC_000003.11:g.52327099C>T, NG_023246.1:g.10264C>T, NM_145262.4:c.1529C>T, NM_145262.3:c.1529C>T, NR_026699.2:n.1619C>T, NR_026699.1:n.1627C>T, NR_026701.2:n.1617C>T, NR_026701.1:n.1625C>T, NM_001144951.2:c.*648C>T, NR_026700.2:n.725C>T, NR_026700.1:n.733C>T, NR_026702.2:n.655C>T, NR_026702.1:n.663C>T, XM_024453351.2:c.1529C>T, XM_024453351.1:c.1529C>T, XM_024453352.2:c.*648C>T, XM_024453352.1:c.*648C>T, XM_017005730.2:c.1148C>T, XM_017005730.1:c.1148C>T, XM_047447465.1:c.1053C>T, XM_047447466.1:c.1053C>T, XM_047447467.1:c.672C>T, NP_660305.2:p.Thr510Ile, XP_024309119.1:p.Thr510Ile, XP_016861219.1:p.Thr383Ile

Select item 148936383312.

rs1489363833 [Homo sapiens]

Variant type:: SNV
Alleles:: C>T [Show Flanks]
Chromosome:: 3:52290241 (GRCh38)
3:52324257 (GRCh37)
Canonical SPDI:: NC_000003.12:52290240:C:T
Gene:: GLYCTK (Varview), GLYCTK-AS1 (Varview)
Functional Consequence:: intron_variant,2KB_upstream_variant,upstream_transcript_variant,5_prime_UTR_variant
Validated:: by frequency,by alfa,by cluster
MAF:: T=0.000108/2 (ALFA)
T=0.000011/3 (TOPMED)
T=0.000014/2 (GnomAD)
T=0.000446/2 (Estonian)
HGVS:: NC_000003.12:g.52290241C>T, NC_000003.11:g.52324257C>T, NG_023246.1:g.7422C>T, XM_024453351.2:c.-102C>T, XM_024453351.1:c.-102C>T, XM_024453352.2:c.-102C>T, XM_024453352.1:c.-102C>T, XM_047447465.1:c.-102C>T

Select item 148823231613.

rs1488232316 [Homo sapiens]

Variant type:: SNV
Alleles:: C>T [Show Flanks]
Chromosome:: 3:52291319 (GRCh38)
3:52325335 (GRCh37)
Canonical SPDI:: NC_000003.12:52291318:C:T
Gene:: GLYCTK (Varview), GLYCTK-AS1 (Varview)
Functional Consequence:: intron_variant,upstream_transcript_variant,2KB_upstream_variant
Validated:: by frequency,by alfa
MAF:: T=0./0 (ALFA)
T=0.000004/1 (TOPMED)
HGVS:: NC_000003.12:g.52291319C>T, NC_000003.11:g.52325335C>T, NG_023246.1:g.8500C>T

Select item 148802901014.

rs1488029010 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A [Show Flanks]
Chromosome:: 3:52289932 (GRCh38)
3:52323948 (GRCh37)
Canonical SPDI:: NC_000003.12:52289931:G:A
Gene:: GLYCTK (Varview), GLYCTK-AS1 (Varview), LOC107986086 (Varview)
Functional Consequence:: intron_variant,2KB_upstream_variant,upstream_transcript_variant,5_prime_UTR_variant
Validated:: by frequency,by alfa
MAF:: A=0./0 (ALFA)
A=0.000004/1 (TOPMED)
HGVS:: NC_000003.12:g.52289932G>A, NC_000003.11:g.52323948G>A, NG_023246.1:g.7113G>A, XM_024453351.2:c.-411G>A, XM_024453351.1:c.-411G>A, XM_024453352.2:c.-411G>A, XM_024453352.1:c.-411G>A, XM_047447465.1:c.-411G>A

Select item 148797802115.

rs1487978021 [Homo sapiens]

Variant type:: SNV
Alleles:: C>T [Show Flanks]
Chromosome:: 3:52289685 (GRCh38)
3:52323701 (GRCh37)
Canonical SPDI:: NC_000003.12:52289684:C:T
Gene:: GLYCTK (Varview), GLYCTK-AS1 (Varview), LOC107986086 (Varview)
Functional Consequence:: intron_variant,2KB_upstream_variant,upstream_transcript_variant,5_prime_UTR_variant,non_coding_transcript_variant
Validated:: by frequency,by alfa
MAF:: T=0./0 (ALFA)
T=0.000007/1 (GnomAD)
HGVS:: NC_000003.12:g.52289685C>T, NC_000003.11:g.52323701C>T, NG_023246.1:g.6866C>T, XM_024453351.2:c.-658C>T, XM_024453351.1:c.-658C>T, XM_024453352.2:c.-658C>T, XM_024453352.1:c.-658C>T, XM_047447465.1:c.-658C>T, NR_046719.1:n.49G>A

Select item 148759394016.

rs1487593940 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A [Show Flanks]
Chromosome:: 3:52294890 (GRCh38)
3:52328906 (GRCh37)
Canonical SPDI:: NC_000003.12:52294889:G:A
Gene:: GLYCTK (Varview), MIR135A1 (Varview)
Functional Consequence:: 2KB_upstream_variant,upstream_transcript_variant,genic_downstream_transcript_variant,3_prime_UTR_variant,non_coding_transcript_variant
Validated:: by frequency
MAF:: A=0.000008/1 (GnomAD_exomes)
HGVS:: NC_000003.12:g.52294890G>A, NC_000003.11:g.52328906G>A, NG_023246.1:g.12071G>A, NM_145262.4:c.*1764G>A, NM_145262.3:c.*1764G>A, NR_026699.2:n.3426G>A, NR_026699.1:n.3434G>A, NR_026701.2:n.3310G>A, NR_026701.1:n.3318G>A, NM_001144951.2:c.*2455G>A, NR_026700.2:n.2418G>A, NR_026700.1:n.2426G>A, NR_026702.2:n.2348G>A, NR_026702.1:n.2356G>A, XM_024453351.2:c.*1764G>A, XM_024453352.2:c.*2455G>A, XM_017005730.2:c.*1764G>A

Select item 148752044917.

rs1487520449 [Homo sapiens]

Variant type:: SNV
Alleles:: C>T [Show Flanks]
Chromosome:: 3:52294130 (GRCh38)
3:52328146 (GRCh37)
Canonical SPDI:: NC_000003.12:52294129:C:T
Gene:: GLYCTK (Varview), MIR135A1 (Varview)
Functional Consequence:: downstream_transcript_variant,genic_downstream_transcript_variant,3_prime_UTR_variant,500B_downstream_variant,non_coding_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: T=0./0 (ALFA)
T=0.000008/2 (TOPMED)
HGVS:: NC_000003.12:g.52294130C>T, NC_000003.11:g.52328146C>T, NG_023246.1:g.11311C>T, NM_145262.4:c.*1004C>T, NM_145262.3:c.*1004C>T, NR_026699.2:n.2666C>T, NR_026699.1:n.2674C>T, NR_026701.2:n.2550C>T, NR_026701.1:n.2558C>T, NM_001144951.2:c.*1695C>T, NR_026700.2:n.1658C>T, NR_026700.1:n.1666C>T, NR_026702.2:n.1588C>T, NR_026702.1:n.1596C>T, XM_024453351.2:c.*1004C>T, XM_024453352.2:c.*1695C>T, XM_017005730.2:c.*1004C>T

Select item 148725661618.

rs1487256616 [Homo sapiens]

Variant type:: SNV
Alleles:: C>T [Show Flanks]
Chromosome:: 3:52291109 (GRCh38)
3:52325125 (GRCh37)
Canonical SPDI:: NC_000003.12:52291108:C:T
Gene:: GLYCTK (Varview), GLYCTK-AS1 (Varview)
Functional Consequence:: coding_sequence_variant,2KB_upstream_variant,missense_variant,upstream_transcript_variant,non_coding_transcript_variant
Validated:: by frequency
MAF:: T=0.000004/1 (GnomAD_exomes)
HGVS:: NC_000003.12:g.52291109C>T, NC_000003.11:g.52325125C>T, NG_023246.1:g.8290C>T, NM_145262.4:c.527C>T, NM_145262.3:c.527C>T, NR_026699.2:n.615C>T, NR_026699.1:n.623C>T, NR_026701.2:n.615C>T, NR_026701.1:n.623C>T, NM_001144951.2:c.527C>T, NM_001144951.1:c.527C>T, NR_026700.2:n.199C>T, NR_026700.1:n.207C>T, NR_026702.2:n.615C>T, NR_026702.1:n.623C>T, XM_024453351.2:c.527C>T, XM_024453351.1:c.527C>T, XM_024453352.2:c.527C>T, XM_024453352.1:c.527C>T, XM_017005730.2:c.146C>T, XM_017005730.1:c.146C>T, XM_047447465.1:c.527C>T, XM_047447466.1:c.527C>T, XM_047447467.1:c.146C>T, NP_660305.2:p.Ser176Leu, NP_001138423.1:p.Ser176Leu, XP_024309119.1:p.Ser176Leu, XP_024309120.1:p.Ser176Leu, XP_016861219.1:p.Ser49Leu, XP_047303421.1:p.Ser176Leu, XP_047303422.1:p.Ser176Leu, XP_047303423.1:p.Ser49Leu

Select item 148703663019.

rs1487036630 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A [Show Flanks]
Chromosome:: 3:52290272 (GRCh38)
3:52324288 (GRCh37)
Canonical SPDI:: NC_000003.12:52290271:G:A
Gene:: GLYCTK (Varview), GLYCTK-AS1 (Varview)
Functional Consequence:: intron_variant,2KB_upstream_variant,upstream_transcript_variant,5_prime_UTR_variant
HGVS:: NC_000003.12:g.52290272G>A, NC_000003.11:g.52324288G>A, NG_023246.1:g.7453G>A, XM_024453351.2:c.-71G>A, XM_024453351.1:c.-71G>A, XM_024453352.2:c.-71G>A, XM_024453352.1:c.-71G>A, XM_047447465.1:c.-71G>A

Select item 148659225720.

rs1486592257 [Homo sapiens]

Variant type:: SNV
Alleles:: C>A [Show Flanks]
Chromosome:: 3:52290886 (GRCh38)
3:52324902 (GRCh37)
Canonical SPDI:: NC_000003.12:52290885:C:A
Gene:: GLYCTK (Varview), GLYCTK-AS1 (Varview)
Functional Consequence:: intron_variant,upstream_transcript_variant,2KB_upstream_variant
Validated:: by frequency,by alfa,by cluster
MAF:: A=0./0 (ALFA)
A=0.000007/1 (GnomAD)
A=0.000008/2 (TOPMED)
HGVS:: NC_000003.12:g.52290886C>A, NC_000003.11:g.52324902C>A, NG_023246.1:g.8067C>A

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