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CLINICAL GENOMICS DATABASE:
HGMD:
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VARIANT EFFECT FUNCTIONAL CLASS IMPACT
DBSNP BUILD:


EXCLUDE VARIANTS AT VARISNP
READ DEPTH:

QUAL:
VARIANTS PER GENE:
SHOW ONLY VARIANTS PRESENT IN COMMON GENES BETWEEN ALL THE INDIVIDUALS SELECTED
SHOW ONLY VARIANTS AT EXACTLY SAME POSITION BETWEEN ALL THE INDIVIDUALS SELECTED
EXCLUDE ALL VARIANTS PRESENT IN LATEST DBSNP BUILD
SHOW ONLY VARIANTS PRESENT AT HGMD

FREQUENCIES

1000 GENOMES FREQUENCY

EXCLUDE ALL VARIANTS PRESENT IN 1000GENOMES
DBSNP FREQUENCY

EXCLUDE ALL VARIANTS PRESENT IN DBSNP
ESP6500 FREQUENCY

EXCLUDE ALL VARIANTS PRESENT IN EXOME SEQUENCING PROJECT

SCORES

SIFT SCORE

EXCLUDE VARIANTS WITHOUT SIFT SCORE
POLYPHEN2 SCORE

EXCLUDE VARIANTS WITHOUT POLYPHEN SCORE
CADD

EXCLUDE VARIANTS WITHOUT CADD SCORE
MCAP

EXCLUDE VARIANTS WITHOUT M-CAP SCORE
OPEN RESULT IN A NEW WINDOW
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Genes at Omim

AP1S1, DNAH11, FAM20C, FLNC, GARS, HOXA13, LAMB1, MAD1L1, NME8, NPC1L1, PEX1, PLOD3, PMS2, PTPN12, RELN, SFRP4, TAF6, TFR2, WDR60,
AP1S1 MEDNIK syndrome, 609313 (3)
DNAH11 Ciliary dyskinesia, primary, 7, with or without situs inversus, 611884 (3)
FAM20C Raine syndrome, 259775 (3)
FLNC Myopathy, myofibrillar, 5, 609524 (3)
Myopathy, distal, 4, 614065 (3)
Cardiomyopathy, familial restrictive 5, 617047 (3)
Cardiomyopathy, familial hypertrophic, 26 (3)
GARS Neuropathy, distal hereditary motor, type VA, 600794 (3)
Charcot-Marie-Tooth disease, type 2D, 601472 (3)
HOXA13 Hand-foot-uterus syndrome, 140000 (3)
Guttmacher syndrome, 176305 (3)
LAMB1 Lissencephaly 5, 615191 (3)
MAD1L1 Prostate cancer, somatic, 176807 (3)
Lymphoma, somatic (3)
NME8 Ciliary dyskinesia, primary, 6, 610852 (3)
NPC1L1 [Ezetimibe, nonresponse to] (3)
PEX1 Peroxisome biogenesis disorder 1B (NALD/IRD), 601539 (3)
Peroxisome biogenesis disorder 1A (Zellweger), 214100 (3)
Heimler syndrome 1, 234580 (3)
PLOD3 Lysyl hydroxylase 3 deficiency, 612394 (3)
PMS2 Mismatch repair cancer syndrome, 276300 (3)
Colorectal cancer, hereditary nonpolyposis, type 4, 614337 (3)
PTPN12 Colon cancer, somatic, 114500 (3)
RELN {Epilepsy, familial temporal lobe, 7}, 616436 (3)
Lissencephaly 2 (Norman-Roberts type), 257320 (3)
SFRP4 Pyle disease, 265900 (3)
TAF6 Alazami-Yuan syndrome, 617126 (3)
TFR2 Hemochromatosis, type 3, 604250 (3)
WDR60 Short-rib thoracic dysplasia 8 with or without polydactyly, 615503 (3)

Genes at Clinical Genomics Database

AP1S1, DNAH11, FAM20C, FLNC, GARS, HOXA13, LAMB1, NME8, NPC1L1, PEX1, PLOD3, PMS2, RELN, SERPINE1, TFR2, WDR60,
AP1S1 MEDNIK syndrome
DNAH11 Ciliary dyskinesia, primary, 7
FAM20C Hypophosphatemia,hyperphosphaturia, dental anomalies, intracerebral calcifications and osteosclerosis (Raine syndrome)
FLNC Myopathy, myofibrillar, 5
Myopathy, distal, 4
GARS Neuropathy, distal hereditary motor, type V
Charcot-Marie-Tooth disease, type 2D
HOXA13 Hand-foot-uterus syndrome
Guttmacher syndrome
Hand-foot-genital syndrome
LAMB1 Lissencephaly 5
NME8 Ciliary dyskinesia, primary, 6
NPC1L1 Ezetimibe, nonresponse to
PEX1 Heimler syndrome 1
PLOD3 Bone fragility with contractures, arterial rupture, and deafness
PMS2 Mismatch repair cancer syndrome
Colorectal cancer, hereditary nonpolyposis type 4
RELN Lissencephaly 2
Epilepsy, familial temporal lobe, 7
SERPINE1 Plasminogen activator inhibitor-1 deficiency
TFR2 Hemochromatosis, type 3
WDR60 Short -rib thoracic dysplasia 8 with or without polydactyly

Genes at HGMD

Summary

Number of Variants: 5928
Number of Genes: 73

Export to: CSV
Omim - GeneCards - NCBI
Options Individual Chr
RsId
Pos
Qual
Ref
Alt
Filter Gen
Read Depth Effect Impact Func Class 1kgenomes dbSNP ESP6500 Sift PP2 CADD M-CAP CLINVAR HI Score
View 23 recalibrated filtered postcgp gqfiltered 7 . 101557767 845.12 A C PASS 0/1 2 None None None None None None None None None None
View 23 recalibrated filtered postcgp gqfiltered 7 . 76532876 28.07 A G PASS 0/1 101 None None None None None None None None None None
View 23 recalibrated filtered postcgp gqfiltered 7 . 76541388 96.09 A C PASS 0/1 15 None None None None None None None None None None
View 23 recalibrated filtered postcgp gqfiltered 7 . 141946634 1639.99 A G PASS 0/1 62 None None None None None None None None None None
View 23 recalibrated filtered postcgp gqfiltered 7 . 151224864 135490.02 A G PASS 1/1 97 None None None None None None None None None None
View 23 recalibrated filtered postcgp gqfiltered 7 . 76611571 5990.05 A G PASS 0/1 86 None None None 0.50 None None None None None None None
View 23 recalibrated filtered postcgp gqfiltered 7 . 141932013 18108.06 A G PASS 1/1 7 None None None None None None None None None None
View 23 recalibrated filtered postcgp gqfiltered 7 . 76625715 90499.18 A G PASS 0/1 52 None None None None None None None None None None
View 23 recalibrated filtered postcgp gqfiltered 7 . 141839065 1548.35 A G PASS 0/1 13 None None None None None None None None None None
View 23 recalibrated filtered postcgp gqfiltered 7 . 76980982 29672.25 A G PASS 0/1 24 None None None None None None None None None None
View 23 recalibrated filtered postcgp gqfiltered 7 . 141838168 38854.19 A G PASS 0/1 35 None None None None None None None None None None
View 23 recalibrated filtered postcgp gqfiltered 7 . 76981090 84521.08 A G PASS 0/1 84 None None None None None None None None None None

PTPN12

Omim - GeneCards - NCBI
Options Individual Chr
RsId
Pos
Qual
Ref
Alt
Filter Gen
Read Depth Effect Impact Func Class 1kgenomes dbSNP ESP6500 Sift PP2 CADD M-CAP CLINVAR HI Score
View 23 recalibrated filtered postcgp gqfiltered 7 . 77256452 113327.14 A G PASS 1/1 59 NON_SYNONYMOUS_CODING MODERATE MISSENSE 0.37 0.01 None None None None None None None
Omim - GeneCards - NCBI
Options Individual Chr
RsId
Pos
Qual
Ref
Alt
Filter Gen
Read Depth Effect Impact Func Class 1kgenomes dbSNP ESP6500 Sift PP2 CADD M-CAP CLINVAR HI Score
View 23 recalibrated filtered postcgp gqfiltered 7 . 77278882 34752.28 A C PASS 0/1 79 None None None None None None None None None None
View 23 recalibrated filtered postcgp gqfiltered 7 . 77286729 77293.11 A G PASS 0/1 6 None None None None None None None None None None
View 23 recalibrated filtered postcgp gqfiltered 7 . 77293230 42796.42 A G PASS 0/1 28 None None None None None None None None None None
View 23 recalibrated filtered postcgp gqfiltered 7 . 77293265 41904.13 A T PASS 0/1 19 None None None None None None None None None None
View 23 recalibrated filtered postcgp gqfiltered 7 . 10932085 2676.75 A G PASS 0/1 154 None None None None None None None None None None
View 23 recalibrated filtered postcgp gqfiltered 7 . 77328509 10952.36 A T PASS 0/1 30 None None None None None None None None None None
View 23 recalibrated filtered postcgp gqfiltered 7 . 11035636 75513.2 A G PASS 1/1 23 None None None None None None None None None None
View 23 recalibrated filtered postcgp gqfiltered 7 . 77329413 139822.34 A G PASS 0/1 58 None None None None None None None None None None
View 23 recalibrated filtered postcgp gqfiltered 7 . 77585642 1197.57 A G PASS 0/1 27 None None None None None None None None None None
View 23 recalibrated filtered postcgp gqfiltered 7 . 141720968 220056.84 A G PASS 0/1 48 None None None None None None None None None None
View 23 recalibrated filtered postcgp gqfiltered 7 . 77736453 53639.48 A G PASS 1/1 34 None None None None None None None None None None
View 23 recalibrated filtered postcgp gqfiltered 7 . 141662893 2878.52 A T PASS 0/1 41 None None None None None None None None None None
View 23 recalibrated filtered postcgp gqfiltered 7 . 77773429 15708.4 A G PASS 0/1 6 None None None None None None None None None None
View 23 recalibrated filtered postcgp gqfiltered 7 . 77778239 8934.3 A G PASS 0/1 20 None None None None None None None None None None
View 23 recalibrated filtered postcgp gqfiltered 7 . 77894204 13619.43 A G PASS 1/1 2 None None None None None None None None None None
View 23 recalibrated filtered postcgp gqfiltered 7 . 77929029 492.79 A G PASS 0/1 8 None None None None None None None None None None
View 23 recalibrated filtered postcgp gqfiltered 7 . 141437754 4375.55 A G PASS 1/1 74 None None None None None None None None None None
View 23 recalibrated filtered postcgp gqfiltered 7 . 11051573 4052.35 A G PASS 0/1 39 None None None None None None None None None None
View 23 recalibrated filtered postcgp gqfiltered 7 . 11376751 1892.78 A G PASS 0/1 9 None None None None None None None None None None
View 23 recalibrated filtered postcgp gqfiltered 7 . 141005999 14.25 A G PASS 0/1 9 None None None None None None None None None None
View 23 recalibrated filtered postcgp gqfiltered 7 . 78489882 70871.55 A C PASS 1/1 39 None None None None None None None None None None
View 23 recalibrated filtered postcgp gqfiltered 7 . 140726457 988.17 A G PASS 0/1 40 None None None None None None None None None None
View 23 recalibrated filtered postcgp gqfiltered 7 . 80511753 16594.36 A G PASS 0/1 28 None None None None None None None None None None
View 23 recalibrated filtered postcgp gqfiltered 7 . 23254127 144432.7 A G PASS 0/1 25 None None None None None None None None None None
View 23 recalibrated filtered postcgp gqfiltered 7 . 80646049 1835.74 A AT PASS 1/1 53 None None None None None None None None None None
View 23 recalibrated filtered postcgp gqfiltered 7 . 140674168 915.63 A G PASS 0/1 91 None None None -0.64 None None None None None None None
View 23 recalibrated filtered postcgp gqfiltered 7 . 80661053 162565.2 A G PASS 1/1 63 None None None None None None None None None None
View 23 recalibrated filtered postcgp gqfiltered 7 . 157669772 1005.18 A G PASS 1/1 6 None None None None None None None None None None
View 23 recalibrated filtered postcgp gqfiltered 7 . 80742511 5735.89 A G PASS 1/1 205 None None None None None None None None None None
View 23 recalibrated filtered postcgp gqfiltered 7 . 80745026 286245.29 A G PASS 1/1 73 None None None None None None None None None None
View 23 recalibrated filtered postcgp gqfiltered 7 . 23260430 111376.7 A C PASS 0/1 14 None None None None None None None None None None
View 23 recalibrated filtered postcgp gqfiltered 7 . 140558041 26640.85 A G PASS 1/1 12 None None None None None None None None None None
View 23 recalibrated filtered postcgp gqfiltered 7 . 150803641 162129.08 A G PASS 0/1 59 None None None -1.57 None None None None None None None
View 23 recalibrated filtered postcgp gqfiltered 7 . 80789373 42616.29 A G PASS 0/1 83 None None None None None None None None None None
View 23 recalibrated filtered postcgp gqfiltered 7 . 140547094 15431.36 A G PASS 1/1 11 None None None None None None None None None None
View 23 recalibrated filtered postcgp gqfiltered 7 . 5977892 25900.95 A G PASS 0/1 10 None None None None None None None None None None
View 23 recalibrated filtered postcgp gqfiltered 7 . 81176065 897.1 A C PASS 0/1 38 None None None None None None None None None None
View 23 recalibrated filtered postcgp gqfiltered 7 . 150803367 41110.06 A G PASS 0/1 60 None None None None None None None None None None
View 23 recalibrated filtered postcgp gqfiltered 7 . 140475228 20.25 A G PASS 0/1 8 None None None None None None None None None None
View 23 recalibrated filtered postcgp gqfiltered 7 . 81709988 20611.52 A C PASS 1/1 31 None None None None None None None None None None
View 23 recalibrated filtered postcgp gqfiltered 7 . 81720892 52064.43 A G PASS 1/1 25 None None None None None None None None None None
View 23 recalibrated filtered postcgp gqfiltered 7 . 81736512 1745.72 A G PASS 0/1 5 None None None None None None None None None None
View 23 recalibrated filtered postcgp gqfiltered 7 . 81742731 13560.07 A G PASS 1/1 64 None None None None None None None None None None
View 23 recalibrated filtered postcgp gqfiltered 7 . 6031484 775.88 A G PASS 0/1 49 None None None -1.40 None None None None None None None
View 23 recalibrated filtered postcgp gqfiltered 7 . 81742840 26879.1 A G PASS 1/1 48 None None None None None None None None None None
View 23 recalibrated filtered postcgp gqfiltered 7 . 23307771 146.89 A C PASS 0/1 14 None None None None None None None None None None
View 23 recalibrated filtered postcgp gqfiltered 7 . 81743136 23688.55 A G PASS 1/1 9 None None None None None None None None None None

PMS2

Omim - GeneCards - NCBI
Options Individual Chr
RsId
Pos
Qual
Ref
Alt
Filter Gen
Read Depth Effect Impact Func Class 1kgenomes dbSNP ESP6500 Sift PP2 CADD M-CAP CLINVAR HI Score
View 23 recalibrated filtered postcgp gqfiltered 7 . 6031646 962.16 A G PASS 0/1 4 SYNONYMOUS_CODING LOW None None None None None None None
Omim - GeneCards - NCBI
Options Individual Chr
RsId
Pos
Qual
Ref
Alt
Filter Gen
Read Depth Effect Impact Func Class 1kgenomes dbSNP ESP6500 Sift PP2 CADD M-CAP CLINVAR HI Score
View 23 recalibrated filtered postcgp gqfiltered 7 . 97858034 5195.06 A G PASS 0/1 42 None None None None None None None None None None
View 23 recalibrated filtered postcgp gqfiltered 7 . 23312938 406.97 A G PASS 0/1 31 None None None None None None None None None None
View 23 recalibrated filtered postcgp gqfiltered 7 . 97859038 18666.29 A G PASS 0/1 21 None None None None None None None None None None
View 23 recalibrated filtered postcgp gqfiltered 7 . 97859257 196081.81 A T PASS 1/1 59 None None None 0.53 None None None None None None None
View 23 recalibrated filtered postcgp gqfiltered 7 . 97869223 22641.32 A G PASS 0/1 13 None None None None None None None None None None
View 23 recalibrated filtered postcgp gqfiltered 7 . 97947461 635.53 A G PASS 0/1 46 None None None None None None None None None None
View 23 recalibrated filtered postcgp gqfiltered 7 . 97984590 1416.78 A G PASS 0/1 86 None None None None None None None None None None
View 23 recalibrated filtered postcgp gqfiltered 7 . 97990156 3267.36 A C PASS 0/1 77 None None None None None None None None None None
View 23 recalibrated filtered postcgp gqfiltered 7 . 140084841 970.95 A G PASS 1/1 13 None None None None None None None None None None
View 23 recalibrated filtered postcgp gqfiltered 7 . 140062482 4462.22 A G PASS 1/1 56 None None None None None None None None None None
View 23 recalibrated filtered postcgp gqfiltered 7 . 140062473 4480.29 A G PASS 1/1 53 None None None None None None None None None None
View 23 recalibrated filtered postcgp gqfiltered 7 . 140026499 12775.74 A AG PASS 1/1 7 None None None None None None None None None None
View 23 recalibrated filtered postcgp gqfiltered 7 . 139913365 62.93 A G PASS 0/1 13 None None None None None None None None None None
View 23 recalibrated filtered postcgp gqfiltered 7 . 98223587 53362.77 A G PASS 1/1 25 None None None None None None None None None None
View 23 recalibrated filtered postcgp gqfiltered 7 . 98903219 30591.31 A G PASS 0/1 15 None None None None None None None None None None
View 23 recalibrated filtered postcgp gqfiltered 7 . 139483814 197.89 A C PASS 0/1 4 None None None None None None None None None None
View 23 recalibrated filtered postcgp gqfiltered 7 . 150801361 10349.06 A AG PASS 0/1 9 None None None None None None None None None None
View 23 recalibrated filtered postcgp gqfiltered 7 . 98983038 1741.18 A G PASS 0/1 15 None None None None None None None None None None
View 23 recalibrated filtered postcgp gqfiltered 7 . 23584856 3038.57 A G PASS 1/1 4 None None None None None None None None None None

ARPC1B

Omim - GeneCards - NCBI
Options Individual Chr
RsId
Pos
Qual
Ref
Alt
Filter Gen
Read Depth Effect Impact Func Class 1kgenomes dbSNP ESP6500 Sift PP2 CADD M-CAP CLINVAR HI Score
View 23 recalibrated filtered postcgp gqfiltered 7 . 98990367 6828.28 A G PASS 0/1 7 NON_SYNONYMOUS_CODING MODERATE MISSENSE 0.03 1.00 None None None None None None None
Omim - GeneCards - NCBI
Options Individual Chr
RsId
Pos
Qual
Ref
Alt
Filter Gen
Read Depth Effect Impact Func Class 1kgenomes dbSNP ESP6500 Sift PP2 CADD M-CAP CLINVAR HI Score
View 23 recalibrated filtered postcgp gqfiltered 7 . 139417752 6170.39 A T PASS 0/1 27 None None None None None None None None None None
View 23 recalibrated filtered postcgp gqfiltered 7 . 139417744 53893.34 A G PASS 1/1 32 None None None None None None None None None None
View 23 recalibrated filtered postcgp gqfiltered 7 . 139412536 42701.47 A AC PASS 1/1 38 None None None None None None None None None None
View 23 recalibrated filtered postcgp gqfiltered 7 . 99040227 16940.43 A G PASS 0/1 27 None None None None None None None None None None
View 23 recalibrated filtered postcgp gqfiltered 7 . 150800839 320.41 A G PASS 0/1 13 None None None None None None None None None None
View 23 recalibrated filtered postcgp gqfiltered 7 . 101037891 110341.0 A G PASS 0/1 274 None None None -1.17 None None None None None None None
View 23 recalibrated filtered postcgp gqfiltered 7 . 101038481 364136.09 A G PASS 0/1 283 None None None None None None None None None None
View 23 recalibrated filtered postcgp gqfiltered 7 . 101038994 112046.0 A G PASS 0/1 300 None None None None None None None None None None

PMS2

Omim - GeneCards - NCBI
Options Individual Chr
RsId
Pos
Qual
Ref
Alt
Filter Gen
Read Depth Effect Impact Func Class 1kgenomes dbSNP ESP6500 Sift PP2 CADD M-CAP CLINVAR HI Score
View 23 recalibrated filtered postcgp gqfiltered 7 . 6038745 37480.1 A C PASS 0/1 46 SYNONYMOUS_CODING LOW None None None None None None None
Omim - GeneCards - NCBI
Options Individual Chr
RsId
Pos
Qual
Ref
Alt
Filter Gen
Read Depth Effect Impact Func Class 1kgenomes dbSNP ESP6500 Sift PP2 CADD M-CAP CLINVAR HI Score
View 23 recalibrated filtered postcgp gqfiltered 7 . 101039772 2057.33 A G PASS 0/1 315 None None None -1.70 None None None None None None None
View 23 recalibrated filtered postcgp gqfiltered 7 . 6048718 21774.65 A G PASS 0/1 21 None None None None None None None None None None
View 23 recalibrated filtered postcgp gqfiltered 7 . 101041269 68598.28 A G PASS 0/1 327 None None None 0.76 None None None None None None None
View 23 recalibrated filtered postcgp gqfiltered 7 . 139138016 20895.69 A G PASS 0/1 7 MOTIF[MA0139.1:CTCF] MODIFIER None None None None None None None
View 23 recalibrated filtered postcgp gqfiltered 7 . 101136895 25216.75 A G PASS 0/1 14 None None None None None None None None None None
View 23 recalibrated filtered postcgp gqfiltered 7 . 101173246 28263.76 A G PASS 1/1 44 None None None None None None None None None None

LUC7L2

Omim - GeneCards - NCBI
Options Individual Chr
RsId
Pos
Qual
Ref
Alt
Filter Gen
Read Depth Effect Impact Func Class 1kgenomes dbSNP ESP6500 Sift PP2 CADD M-CAP CLINVAR HI Score
View 23 recalibrated filtered postcgp gqfiltered 7 . 139060862 580.63 A G PASS 0/1 61 NON_SYNONYMOUS_CODING MODERATE MISSENSE 0.14 0.93 None None None None None None None
Omim - GeneCards - NCBI
Options Individual Chr
RsId
Pos
Qual
Ref
Alt
Filter Gen
Read Depth Effect Impact Func Class 1kgenomes dbSNP ESP6500 Sift PP2 CADD M-CAP CLINVAR HI Score
View 23 recalibrated filtered postcgp gqfiltered 7 . 101174395 16132.28 A G PASS 1/1 14 None None None None None None None None None None
View 23 recalibrated filtered postcgp gqfiltered 7 . 101174820 56734.67 A G PASS 1/1 89 None None None None None None None None None None
View 23 recalibrated filtered postcgp gqfiltered 7 . 101180110 256.85 A G PASS 1/1 1 None None None None None None None None None None