SNP Links for Protein (Select 21313638) - SNP

Links from Protein

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Select item 14899682111.

rs1489968211 [Homo sapiens]

Variant type:: SNV
Alleles:: A>T [Show Flanks]
Chromosome:: 4:25018133 (GRCh38)
4:25019755 (GRCh37)
Canonical SPDI:: NC_000004.12:25018132:A:T
Gene:: LGI2 (Varview), LOC102723675 (Varview)
Functional Consequence:: genic_downstream_transcript_variant,missense_variant,intron_variant,coding_sequence_variant
Validated:: by frequency,by alfa
MAF:: T=0./0 (ALFA)
T=0.000004/1 (TOPMED)
HGVS:: NC_000004.12:g.25018133A>T, NC_000004.11:g.25019755A>T, NM_018176.4:c.511T>A, NM_018176.3:c.511T>A, XM_011513850.3:c.511T>A, XM_011513850.2:c.511T>A, XM_011513850.1:c.511T>A, XM_017008356.2:c.511T>A, XM_017008356.1:c.511T>A, NP_060646.2:p.Cys171Ser, XP_011512152.1:p.Cys171Ser, XP_016863845.1:p.Cys171Ser

Select item 14871584472.

rs1487158447 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A [Show Flanks]
Chromosome:: 4:25028529 (GRCh38)
4:25030151 (GRCh37)
Canonical SPDI:: NC_000004.12:25028528:G:A
Gene:: LGI2 (Varview), LOC124900684 (Varview)
Functional Consequence:: missense_variant,coding_sequence_variant,upstream_transcript_variant,2KB_upstream_variant
HGVS:: NC_000004.12:g.25028529G>A, NC_000004.11:g.25030151G>A, NM_018176.4:c.247C>T, NM_018176.3:c.247C>T, XM_011513850.3:c.247C>T, XM_011513850.2:c.247C>T, XM_011513850.1:c.247C>T, XM_017008356.2:c.247C>T, XM_017008356.1:c.247C>T, NP_060646.2:p.His83Tyr, XP_011512152.1:p.His83Tyr, XP_016863845.1:p.His83Tyr

Select item 14856628893.

rs1485662889 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A [Show Flanks]
Chromosome:: 4:25028531 (GRCh38)
4:25030153 (GRCh37)
Canonical SPDI:: NC_000004.12:25028530:G:A
Gene:: LGI2 (Varview), LOC124900684 (Varview)
Functional Consequence:: missense_variant,coding_sequence_variant,upstream_transcript_variant,2KB_upstream_variant
Validated:: by frequency,by alfa,by cluster
MAF:: A=0./0 (ALFA)
A=0.000004/1 (TOPMED)
A=0.000007/1 (GnomAD)
HGVS:: NC_000004.12:g.25028531G>A, NC_000004.11:g.25030153G>A, NM_018176.4:c.245C>T, NM_018176.3:c.245C>T, XM_011513850.3:c.245C>T, XM_011513850.2:c.245C>T, XM_011513850.1:c.245C>T, XM_017008356.2:c.245C>T, XM_017008356.1:c.245C>T, NP_060646.2:p.Ser82Phe, XP_011512152.1:p.Ser82Phe, XP_016863845.1:p.Ser82Phe

Select item 14835661464.

rs1483566146 [Homo sapiens]

Variant type:: SNV
Alleles:: C>T [Show Flanks]
Chromosome:: 4:25004099 (GRCh38)
4:25005721 (GRCh37)
Canonical SPDI:: NC_000004.12:25004098:C:T
Gene:: LGI2 (Varview), LOC102723675 (Varview)
Functional Consequence:: coding_sequence_variant,intron_variant,genic_downstream_transcript_variant,synonymous_variant,non_coding_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: T=0.000028/1 (ALFA)
T=0.000004/1 (GnomAD_exomes)
T=0.000007/1 (GnomAD)
T=0.000026/7 (TOPMED)
HGVS:: NC_000004.12:g.25004099C>T, NC_000004.11:g.25005721C>T, NM_018176.4:c.990G>A, NM_018176.3:c.990G>A, XR_001741618.3:n.8485C>T, XR_001741618.2:n.8485C>T

Select item 14819089585.

rs1481908958 [Homo sapiens]

Variant type:: DELINS
Alleles:: C>- [Show Flanks]
Chromosome:: 4:25004212 (GRCh38)
4:25005834 (GRCh37)
Canonical SPDI:: NC_000004.12:25004211:CC:C
Gene:: LGI2 (Varview), LOC102723675 (Varview)
Functional Consequence:: coding_sequence_variant,intron_variant,genic_downstream_transcript_variant,stop_gained,non_coding_transcript_variant
HGVS:: NC_000004.12:g.25004213del, NC_000004.11:g.25005835del, NM_018176.4:c.877del, NM_018176.3:c.877del, XR_001741618.3:n.8599del, XR_001741618.2:n.8599del, NP_060646.2:p.Val292_Val293insTer

Select item 14791635356.

rs1479163535 [Homo sapiens]

Variant type:: SNV
Alleles:: T>C [Show Flanks]
Chromosome:: 4:25004109 (GRCh38)
4:25005731 (GRCh37)
Canonical SPDI:: NC_000004.12:25004108:T:C
Gene:: LGI2 (Varview), LOC102723675 (Varview)
Functional Consequence:: missense_variant,coding_sequence_variant,intron_variant,genic_downstream_transcript_variant,non_coding_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: C=0./0 (ALFA)
C=0.000004/1 (TOPMED)
C=0.000008/2 (GnomAD_exomes)
C=0.000014/2 (GnomAD)
HGVS:: NC_000004.12:g.25004109T>C, NC_000004.11:g.25005731T>C, NM_018176.4:c.980A>G, NM_018176.3:c.980A>G, XR_001741618.3:n.8495T>C, XR_001741618.2:n.8495T>C, NP_060646.2:p.Asn327Ser

Select item 14775640807.

rs1477564080 [Homo sapiens]

Variant type:: SNV
Alleles:: C>A [Show Flanks]
Chromosome:: 4:25030529 (GRCh38)
4:25032151 (GRCh37)
Canonical SPDI:: NC_000004.12:25030528:C:A
Gene:: LGI2 (Varview), LOC124900684 (Varview)
Functional Consequence:: intron_variant,coding_sequence_variant,synonymous_variant
HGVS:: NC_000004.12:g.25030529C>A, NC_000004.11:g.25032151C>A, NM_018176.4:c.165G>T, NM_018176.3:c.165G>T, XM_011513850.3:c.165G>T, XM_011513850.2:c.165G>T, XM_011513850.1:c.165G>T, XM_017008356.2:c.165G>T, XM_017008356.1:c.165G>T

Select item 14758894058.

rs1475889405 [Homo sapiens]

Variant type:: SNV
Alleles:: C>T [Show Flanks]
Chromosome:: 4:25030643 (GRCh38)
4:25032265 (GRCh37)
Canonical SPDI:: NC_000004.12:25030642:C:T
Gene:: LGI2 (Varview), LOC124900684 (Varview)
Functional Consequence:: coding_sequence_variant,intron_variant,synonymous_variant
HGVS:: NC_000004.12:g.25030643C>T, NC_000004.11:g.25032265C>T, NM_018176.4:c.51G>A, NM_018176.3:c.51G>A, XM_011513850.3:c.51G>A, XM_011513850.2:c.51G>A, XM_011513850.1:c.51G>A, XM_017008356.2:c.51G>A, XM_017008356.1:c.51G>A

Select item 14750461319.

rs1475046131 [Homo sapiens]

Variant type:: SNV
Alleles:: T>G [Show Flanks]
Chromosome:: 4:25003948 (GRCh38)
4:25005570 (GRCh37)
Canonical SPDI:: NC_000004.12:25003947:T:G
Gene:: LGI2 (Varview), LOC102723675 (Varview)
Functional Consequence:: missense_variant,genic_downstream_transcript_variant,intron_variant,coding_sequence_variant,non_coding_transcript_variant
Validated:: by frequency
MAF:: G=0.000004/1 (GnomAD_exomes)
HGVS:: NC_000004.12:g.25003948T>G, NC_000004.11:g.25005570T>G, NM_018176.4:c.1141A>C, NM_018176.3:c.1141A>C, XR_001741618.3:n.8334T>G, XR_001741618.2:n.8334T>G, NP_060646.2:p.Ile381Leu

Select item 147406388710.

rs1474063887 [Homo sapiens]

Variant type:: SNV
Alleles:: T>G [Show Flanks]
Chromosome:: 4:25003591 (GRCh38)
4:25005213 (GRCh37)
Canonical SPDI:: NC_000004.12:25003590:T:G
Gene:: LGI2 (Varview), LOC102723675 (Varview)
Functional Consequence:: missense_variant,genic_downstream_transcript_variant,intron_variant,coding_sequence_variant,non_coding_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: G=0./0 (ALFA)
G=0.000004/1 (TOPMED)
G=0.000008/2 (GnomAD_exomes)
HGVS:: NC_000004.12:g.25003591T>G, NC_000004.11:g.25005213T>G, NM_018176.4:c.1498A>C, NM_018176.3:c.1498A>C, XR_001741618.3:n.7977T>G, XR_001741618.2:n.7977T>G, NP_060646.2:p.Lys500Gln

Select item 147377222811.

rs1473772228 [Homo sapiens]

Variant type:: SNV
Alleles:: C>A,T [Show Flanks]
Chromosome:: 4:25003487 (GRCh38)
4:25005109 (GRCh37)
Canonical SPDI:: NC_000004.12:25003486:C:A,NC_000004.12:25003486:C:T
Gene:: LGI2 (Varview), LOC102723675 (Varview)
Functional Consequence:: synonymous_variant,missense_variant,genic_downstream_transcript_variant,intron_variant,coding_sequence_variant,non_coding_transcript_variant
Validated:: by frequency,by alfa,by cluster
MAF:: T=0./0 (ALFA)
T=0.000004/1 (GnomAD_exomes)
T=0.000019/5 (TOPMED)
T=0.000021/3 (GnomAD)
HGVS:: NC_000004.12:g.25003487C>A, NC_000004.12:g.25003487C>T, NC_000004.11:g.25005109C>A, NC_000004.11:g.25005109C>T, NM_018176.4:c.1602G>T, NM_018176.4:c.1602G>A, NM_018176.3:c.1602G>T, NM_018176.3:c.1602G>A, XR_001741618.3:n.7873C>A, XR_001741618.3:n.7873C>T, XR_001741618.2:n.7873C>A, XR_001741618.2:n.7873C>T, NP_060646.2:p.Lys534Asn

Select item 147149911612.

rs1471499116 [Homo sapiens]

Variant type:: SNV
Alleles:: A>T [Show Flanks]
Chromosome:: 4:25003978 (GRCh38)
4:25005600 (GRCh37)
Canonical SPDI:: NC_000004.12:25003977:A:T
Gene:: LGI2 (Varview), LOC102723675 (Varview)
Functional Consequence:: missense_variant,genic_downstream_transcript_variant,intron_variant,coding_sequence_variant,non_coding_transcript_variant
Validated:: by frequency,by cluster
MAF:: T=0.000007/1 (GnomAD)
HGVS:: NC_000004.12:g.25003978A>T, NC_000004.11:g.25005600A>T, NM_018176.4:c.1111T>A, NM_018176.3:c.1111T>A, XR_001741618.3:n.8364A>T, XR_001741618.2:n.8364A>T, NP_060646.2:p.Phe371Ile

Select item 146988526413.

rs1469885264 [Homo sapiens]

Variant type:: SNV
Alleles:: C>A [Show Flanks]
Chromosome:: 4:25030524 (GRCh38)
4:25032146 (GRCh37)
Canonical SPDI:: NC_000004.12:25030523:C:A
Gene:: LGI2 (Varview), LOC124900684 (Varview)
Functional Consequence:: missense_variant,coding_sequence_variant,intron_variant
HGVS:: NC_000004.12:g.25030524C>A, NC_000004.11:g.25032146C>A, NM_018176.4:c.170G>T, NM_018176.3:c.170G>T, XM_011513850.3:c.170G>T, XM_011513850.2:c.170G>T, XM_011513850.1:c.170G>T, XM_017008356.2:c.170G>T, XM_017008356.1:c.170G>T, NP_060646.2:p.Arg57Met, XP_011512152.1:p.Arg57Met, XP_016863845.1:p.Arg57Met

Select item 146587189914.

rs1465871899 [Homo sapiens]

Variant type:: SNV
Alleles:: C>T [Show Flanks]
Chromosome:: 4:25030544 (GRCh38)
4:25032166 (GRCh37)
Canonical SPDI:: NC_000004.12:25030543:C:T
Gene:: LGI2 (Varview), LOC124900684 (Varview)
Functional Consequence:: coding_sequence_variant,intron_variant,synonymous_variant
HGVS:: NC_000004.12:g.25030544C>T, NC_000004.11:g.25032166C>T, NM_018176.4:c.150G>A, NM_018176.3:c.150G>A, XM_011513850.3:c.150G>A, XM_011513850.2:c.150G>A, XM_011513850.1:c.150G>A, XM_017008356.2:c.150G>A, XM_017008356.1:c.150G>A

Select item 146339654815.

rs1463396548 has merged into rs761373892 [Homo sapiens]

Variant type:: DELINS
Alleles:: AGCAGC>-,AGC,AGCAGCAGC,AGCAGCAGCAGC [Show Flanks]
Chromosome:: 4:25030653 (GRCh38)
4:25032275 (GRCh37)
Canonical SPDI:: NC_000004.12:25030639:CAGCAGCAGCAGCAGCAGC:CAGCAGCAGCAGC,NC_000004.12:25030639:CAGCAGCAGCAGCAGCAGC:CAGCAGCAGCAGCAGC,NC_000004.12:25030639:CAGCAGCAGCAGCAGCAGC:CAGCAGCAGCAGCAGCAGCAGC,NC_000004.12:25030639:CAGCAGCAGCAGCAGCAGC:CAGCAGCAGCAGCAGCAGCAGCAGC
Gene:: LGI2 (Varview), LOC124900684 (Varview)
Functional Consequence:: inframe_deletion,inframe_insertion,coding_sequence_variant,intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: CAGCAGCAGCAGC=0.000034/3 (ALFA)
CAG=0.000177/3 (TOMMO)
CAG=0.0002/53 (TOPMED)
-=0.051892/491 (GoESP)
HGVS:: NC_000004.12:g.25030641AGC[4], NC_000004.12:g.25030641AGC[5], NC_000004.12:g.25030641AGC[7], NC_000004.12:g.25030641AGC[8], NC_000004.11:g.25032263AGC[4], NC_000004.11:g.25032263AGC[5], NC_000004.11:g.25032263AGC[7], NC_000004.11:g.25032263AGC[8], NM_018176.4:c.37CTG[4], NM_018176.4:c.37CTG[5], NM_018176.4:c.37CTG[7], NM_018176.4:c.37CTG[8], NM_018176.3:c.37CTG[4], NM_018176.3:c.37CTG[5], NM_018176.3:c.37CTG[7], NM_018176.3:c.37CTG[8], XM_011513850.3:c.37CTG[4], XM_011513850.3:c.37CTG[5], XM_011513850.3:c.37CTG[7], XM_011513850.3:c.37CTG[8], XM_011513850.2:c.37CTG[4], XM_011513850.2:c.37CTG[5], XM_011513850.2:c.37CTG[7], XM_011513850.2:c.37CTG[8], XM_011513850.1:c.37CTG[4], XM_011513850.1:c.37CTG[5], XM_011513850.1:c.37CTG[7], XM_011513850.1:c.37CTG[8], XM_017008356.2:c.37CTG[4], XM_017008356.2:c.37CTG[5], XM_017008356.2:c.37CTG[7], XM_017008356.2:c.37CTG[8], XM_017008356.1:c.37CTG[4], XM_017008356.1:c.37CTG[5], XM_017008356.1:c.37CTG[7], XM_017008356.1:c.37CTG[8], NP_060646.2:p.Leu17_Leu18del, NP_060646.2:p.Leu18del, NP_060646.2:p.Leu18dup, NP_060646.2:p.Leu17_Leu18dup, XP_011512152.1:p.Leu17_Leu18del, XP_011512152.1:p.Leu18del, XP_011512152.1:p.Leu18dup, XP_011512152.1:p.Leu17_Leu18dup, XP_016863845.1:p.Leu17_Leu18del, XP_016863845.1:p.Leu18del, XP_016863845.1:p.Leu18dup, XP_016863845.1:p.Leu17_Leu18dup

Select item 145953072016.

rs1459530720 [Homo sapiens]

Variant type:: DELINS
Alleles:: AAA>-,AAAA [Show Flanks]
Chromosome:: 4:25003517 (GRCh38)
4:25005139 (GRCh37)
Canonical SPDI:: NC_000004.12:25003513:AAAAAA:AAA,NC_000004.12:25003513:AAAAAA:AAAAAAA
Gene:: LGI2 (Varview), LOC102723675 (Varview)
Functional Consequence:: inframe_deletion,frameshift_variant,coding_sequence_variant,non_coding_transcript_variant,genic_downstream_transcript_variant,intron_variant
Validated:: by frequency,by alfa,by cluster
MAF:: AAAAAAA=0./0 (ALFA)
-=0.000004/1 (GnomAD_exomes)
A=0.000004/1 (TOPMED)
A=0.000014/2 (GnomAD)
HGVS:: NC_000004.12:g.25003517_25003519del, NC_000004.12:g.25003519dup, NC_000004.11:g.25005139_25005141del, NC_000004.11:g.25005141dup, NM_018176.4:c.1573_1575del, NM_018176.4:c.1575dup, NM_018176.3:c.1573_1575del, NM_018176.3:c.1575dup, XR_001741618.3:n.7903_7905del, XR_001741618.3:n.7905dup, XR_001741618.2:n.7903_7905del, XR_001741618.2:n.7905dup, NP_060646.2:p.Phe525del, NP_060646.2:p.Ala526fs

Select item 145828974917.

rs1458289749 [Homo sapiens]

Variant type:: SNV
Alleles:: T>C [Show Flanks]
Chromosome:: 4:25003808 (GRCh38)
4:25005430 (GRCh37)
Canonical SPDI:: NC_000004.12:25003807:T:C
Gene:: LGI2 (Varview), LOC102723675 (Varview)
Functional Consequence:: coding_sequence_variant,non_coding_transcript_variant,synonymous_variant,genic_downstream_transcript_variant,intron_variant
HGVS:: NC_000004.12:g.25003808T>C, NC_000004.11:g.25005430T>C, NM_018176.4:c.1281A>G, NM_018176.3:c.1281A>G, XR_001741618.3:n.8194T>C, XR_001741618.2:n.8194T>C

Select item 145688687218.

rs1456886872 [Homo sapiens]

Variant type:: SNV
Alleles:: T>C [Show Flanks]
Chromosome:: 4:25026921 (GRCh38)
4:25028543 (GRCh37)
Canonical SPDI:: NC_000004.12:25026920:T:C
Gene:: LGI2 (Varview), LOC102723675 (Varview)
Functional Consequence:: 500B_downstream_variant,downstream_transcript_variant,synonymous_variant,coding_sequence_variant
Validated:: by frequency
MAF:: C=0.000004/1 (GnomAD_exomes)
HGVS:: NC_000004.12:g.25026921T>C, NC_000004.11:g.25028543T>C, NM_018176.4:c.288A>G, NM_018176.3:c.288A>G, XM_011513850.3:c.288A>G, XM_011513850.2:c.288A>G, XM_011513850.1:c.288A>G, XM_017008356.2:c.288A>G, XM_017008356.1:c.288A>G

Select item 145511518919.

rs1455115189 [Homo sapiens]

Variant type:: SNV
Alleles:: G>T [Show Flanks]
Chromosome:: 4:25026928 (GRCh38)
4:25028550 (GRCh37)
Canonical SPDI:: NC_000004.12:25026927:G:T
Gene:: LGI2 (Varview), LOC102723675 (Varview)
Functional Consequence:: 500B_downstream_variant,downstream_transcript_variant,coding_sequence_variant,missense_variant
Validated:: by frequency
MAF:: T=0.000004/1 (GnomAD_exomes)
HGVS:: NC_000004.12:g.25026928G>T, NC_000004.11:g.25028550G>T, NM_018176.4:c.281C>A, NM_018176.3:c.281C>A, XM_011513850.3:c.281C>A, XM_011513850.2:c.281C>A, XM_011513850.1:c.281C>A, XM_017008356.2:c.281C>A, XM_017008356.1:c.281C>A, NP_060646.2:p.Ser94Tyr, XP_011512152.1:p.Ser94Tyr, XP_016863845.1:p.Ser94Tyr

Select item 145103594220.

rs1451035942 [Homo sapiens]

Variant type:: SNV
Alleles:: G>A [Show Flanks]
Chromosome:: 4:25030613 (GRCh38)
4:25032235 (GRCh37)
Canonical SPDI:: NC_000004.12:25030612:G:A
Gene:: LGI2 (Varview), LOC124900684 (Varview)
Functional Consequence:: intron_variant,synonymous_variant,coding_sequence_variant
HGVS:: NC_000004.12:g.25030613G>A, NC_000004.11:g.25032235G>A, NM_018176.4:c.81C>T, NM_018176.3:c.81C>T, XM_011513850.3:c.81C>T, XM_011513850.2:c.81C>T, XM_011513850.1:c.81C>T, XM_017008356.2:c.81C>T, XM_017008356.1:c.81C>T

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