Evidence finder variant level

This table provides links to genetic databases ClinVar and HGMD for variants reported as GoF/LoF. This data was compiled from the work of (Bayrak et al., 2021) doi: 10.1016/j.ajhg.2021.10.007 in addition to ClinVar/HGMD. Some data has been simplified or omitted to produce a responsive reference table. For extended information including the evidence summary see external links.

Last update: 2021-11-25

Show gene-level evidence from ClinGen.

Gene
Label
Chr
Pos
Database
RefSeqVar
HGVSc
HGVSp
MAX_AF
HGMD
RefSeq
cDNA_position
CDS_position
Protein_position
Consequence
IMPACT
Variant class
SIFT
PolyPhen
Condel
CADD_PHRED
REVEL
LoFtool
ExACpLI
Selective pressure
CDS_len
No. of paralogs
denovo
Essentiality
RVIS
GDI_Phred
MSC_95CI
Inheritance
Amino_acids
IUPRED2
ANCHOR2
RSA
Zfit
RSA_class
helix_prob
beta_prob
coil_prob
Pfam_dom
DOMAINS_VEP
Clarks_distance
ClinVar
Ref
Alt
GNB1
GOF
1
1735987
HGMD + ClinVar
NM_002074.5(GNB1):c.301A>G (p.Met101Val)
ENST00000378609.4:c.301A>G
ENSP00000367872.3:p.Met101Val
​
CM164925
NM_002074.4
633/3128
301/1023
101/340
missense_variant
MODERATE
SNV
deleterious(0)
possibly_damaging(0.527)
deleterious(0.623)
24
0.515
​
1
0.00793
1023
5
3.415877219
0.872602264
-0.32
0.01624
​
AD
M/V
0.1349
0.2137
0.179
1.444
B
0.001
0.959
0.04
PF00400
PROSITE_profiles:PS50294,hmmpanther:PTHR19850,Gene3D:2.130.10.10,Pfam_domain:PF00400,PIRSF_domain:PIRSF002394,SMART_domains:SM00320,Superfamily_domains:SSF50978,Prints_domain:PR00319
1.05855
226496
T
C
GNB1
GOF
1
1736004
HGMD + ClinVar
NM_002074.5(GNB1):c.284T>C (p.Leu95Pro)
ENST00000378609.4:c.284T>C
ENSP00000367872.3:p.Leu95Pro
​
CM164934
NM_002074.4
616/3128
284/1023
95/340
missense_variant
MODERATE
SNV
deleterious(0)
probably_damaging(0.997)
deleterious(0.911)
32
0.555
​
1
0.00793
1023
5
3.415877219
0.872602264
-0.32
0.01624
​
AD
L/P
0.1028
0.21
0.211
-0.695
B
0.004
0.138
0.858
Outside_domain
PROSITE_profiles:PS50294,hmmpanther:PTHR19850,Gene3D:2.130.10.10,PIRSF_domain:PIRSF002394,SMART_domains:SM00320,Superfamily_domains:SSF50978,Prints_domain:PR00319
1.05855
226497
A
G
GNB1
GOF
1
1737948
HGMD + ClinVar
NM_002074.5(GNB1):c.233A>G (p.Lys78Arg)
ENST00000378609.4:c.233A>G
ENSP00000367872.3:p.Lys78Arg
​
CM164917
NM_002074.4
565/3128
233/1023
78/340
missense_variant
MODERATE
SNV
tolerated(0.07)
possibly_damaging(0.889)
deleterious(0.668)
23.9
0.309
​
1
0.00793
1023
5
3.415877219
0.872602264
-0.32
0.01624
​
AD
K/R
0.1399
0.2796
0.097
0.891
B
0.003
0.718
0.279
PF00400
PROSITE_profiles:PS50082,PROSITE_profiles:PS50294,hmmpanther:PTHR19850,PROSITE_patterns:PS00678,Gene3D:2.130.10.10,Pfam_domain:PF00400,PIRSF_domain:PIRSF002394,SMART_domains:SM00320,Superfamily_domains:SSF50978,Prints_domain:PR00320,Prints_domain:PR00319
1.05855
226499
T
C
GNB1
GOF
1
1737952
HGMD + ClinVar
NM_002074.5(GNB1):c.229G>A (p.Gly77Ser)
ENST00000378609.4:c.229G>A
ENSP00000367872.3:p.Gly77Ser
0
CM164933
NM_002074.4
561/3128
229/1023
77/340
missense_variant
MODERATE
SNV
deleterious(0)
possibly_damaging(0.89)
deleterious(0.794)
34
0.668
​
1
0.00793
1023
5
3.415877219
0.872602264
-0.32
0.01624
​
AD
G/S
0.1298
0.2873
0.147
0.402
B
0.005
0.015
0.979
PF00400
PROSITE_profiles:PS50082,PROSITE_profiles:PS50294,hmmpanther:PTHR19850,PROSITE_patterns:PS00678,Gene3D:2.130.10.10,Pfam_domain:PF00400,PIRSF_domain:PIRSF002394,SMART_domains:SM00320,Superfamily_domains:SSF50978,Prints_domain:PR00320,Prints_domain:PR00319
1.05855
226500
C
T
GNB1
GOF
1
1737953
HGMD + ClinVar
NM_002074.5(GNB1):c.228T>G (p.Asp76Glu)
ENST00000378609.4:c.228T>G
ENSP00000367872.3:p.Asp76Glu
​
CM164931
NM_002074.4
560/3128
228/1023
76/340
missense_variant
MODERATE
SNV
deleterious(0)
possibly_damaging(0.766)
deleterious(0.728)
23.6
0.796
​
1
0.00793
1023
5
3.415877219
0.872602264
-0.32
0.01624
​
AD
D/E
0.1349
0.2944
0.167
-0.696
B
0.003
0.003
0.994
PF00400
PROSITE_profiles:PS50082,PROSITE_profiles:PS50294,hmmpanther:PTHR19850,PROSITE_patterns:PS00678,Gene3D:2.130.10.10,Pfam_domain:PF00400,PIRSF_domain:PIRSF002394,SMART_domains:SM00320,Superfamily_domains:SSF50978,Prints_domain:PR00320,Prints_domain:PR00319
1.05855
226501
A
C
GNB1
GOF
1
1737954
HGMD + ClinVar
NM_002074.5(GNB1):c.227A>G (p.Asp76Gly)
ENST00000378609.4:c.227A>G
ENSP00000367872.3:p.Asp76Gly
​
CM164914
NM_002074.4
559/3128
227/1023
76/340
missense_variant
MODERATE
SNV
deleterious(0)
possibly_damaging(0.664)
deleterious(0.679)
31
0.906
​
1
0.00793
1023
5
3.415877219
0.872602264
-0.32
0.01624
​
AD
D/G
0.1349
0.2944
0.167
-0.696
B
0.003
0.003
0.994
PF00400
PROSITE_profiles:PS50082,PROSITE_profiles:PS50294,hmmpanther:PTHR19850,PROSITE_patterns:PS00678,Gene3D:2.130.10.10,Pfam_domain:PF00400,PIRSF_domain:PIRSF002394,SMART_domains:SM00320,Superfamily_domains:SSF50978,Prints_domain:PR00320,Prints_domain:PR00319
1.05855
226502
T
C
PIK3CD
GOF
1
9779982
HGMD + ClinVar
NM_005026.5(PIK3CD):c.1246T>C (p.Cys416Arg)
ENST00000377346.4:c.1246T>C
ENSP00000366563.4:p.Cys416Arg
​
CM143040
NM_005026.4
1441/5203
1246/3135
416/1044
missense_variant
MODERATE
SNV
tolerated(0.26)
possibly_damaging(0.88)
neutral(0.377)
23.7
0.82
0.183
1
0.04588
3207
7
3.857967127
0.995228052
-1.66
3.55263
24.2
UNK
C/R
0.1373
0.2012
0.268
0.394
B
0.021
0.279
0.699
PF00792
Gene3D:2.60.40.150,Pfam_domain:PF00792,PROSITE_profiles:PS51547,hmmpanther:PTHR10048,hmmpanther:PTHR10048:SF35,Superfamily_domains:SSF49562
0.44895
136557
T
C
PIK3CD
GOF
1
9780851
HGMD + ClinVar
NM_005026.5(PIK3CD):c.1573G>A (p.Glu525Lys)
ENST00000377346.4:c.1573G>A
ENSP00000366563.4:p.Glu525Lys
​
CM1310847
NM_005026.4
1768/5203
1573/3135
525/1044
missense_variant
MODERATE
SNV
deleterious(0)
possibly_damaging(0.794)
deleterious(0.742)
26
0.4
0.183
1
0.04588
3207
7
3.857967127
0.995228052
-1.66
3.55263
24.2
UNK
E/K
0.1671
0.3139
0.68
0.684
E
0.97
0.001
0.029
PF00613
Gene3D:1.25.40.70,Pfam_domain:PF00613,PROSITE_profiles:PS51545,hmmpanther:PTHR10048,hmmpanther:PTHR10048:SF35,SMART_domains:SM00145,Superfamily_domains:SSF48371
0.44895
136556
G
A
TARDBP
GOF
1
11082494
HGMD + ClinVar
NM_007375.3(TARDBP):c.1028A>G (p.Gln343Arg)
ENST00000240185.3:c.1028A>G
ENSP00000240185.3:p.Gln343Arg
​
CM085732
NM_007375.3
1142/2748
1028/1245
343/414
missense_variant
MODERATE
SNV
deleterious(0.04)
possibly_damaging(0.901)
deleterious(0.706)
10.21
0.766
​
0.98
0.00789
1245
3
2.412533227
0.895314001
-0.38
0.07842
0.089
AD
Q/R
0.6906
0.5633
0.089
-3.13
B
0.053
0.043
0.903
Outside_domain
Low_complexity_(Seg):seg,hmmpanther:PTHR24011:SF67,hmmpanther:PTHR24011
0.92472
20274
A
G
TARDBP
GOF
1
11082501
HGMD + ClinVar
NM_007375.3(TARDBP):c.1035C>A (p.Asn345Lys)
ENST00000240185.3:c.1035C>A
ENSP00000240185.3:p.Asn345Lys
0.000018
CM085730
NM_007375.3
1149/2748
1035/1245
345/414
missense_variant
MODERATE
SNV
tolerated(0.16)
benign(0.011)
neutral(0.060)
14.46
0.341
​
0.98
0.00789
1245
3
2.412533227
0.895314001
-0.38
0.07842
0.089
AD
N/K
0.8013
0.4685
0.113
-2.657
B
0.053
0.043
0.903
Outside_domain
Low_complexity_(Seg):seg,hmmpanther:PTHR24011:SF67,hmmpanther:PTHR24011
0.92472
34319
C
A
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References

  1. Bayrak, C. S., Stein, D., Jain, A., Chaudhary, K., Nadkarni, G. N., Van Vleck, T. T., Puel, A., Boisson-Dupuis, S., Okada, S., Stenson, P. D., & others. (2021). Identification of discriminative gene-level and protein-level features associated with pathogenic gain-of-function and loss-of-function variants. The American Journal of Human Genetics.