+ Filter Options

SELECT VARIANTS FROM EXCLUDE VARIANTS FROM
INDIVIDUALS:

SNP LIST:
 GROUPS:

SAVED GENE LIST:

GENE LIST:
INDIVIDUALS:

EXCLUDE SNP LIST:
 EXCLUDE GROUPS:

EXCLUDE SAVED GENE LIST:

EXCLUDE GENE LIST:
SELECT YOUR DISEASES:
OMIM:
CLINICAL GENOMICS DATABASE:
HGMD:
MUTATION TYPE:
 CHR:

POS:
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
RESET FILTER | Save Config | Save Analysis

+ Genes 4

Genes:
COL2A1, KERA, KRT3, PXN,

+ Genes associated with diseases 3

Genes at Omim

COL2A1, KERA, KRT3,
COL2A1 Avascular necrosis of the femoral head, 608805 (3)
Czech dysplasia, 609162 (3)
Epiphyseal dysplasia, multiple, with myopia and deafness, 132450 (3)
Kniest dysplasia, 156550 (3)
Legg-Calve-Perthes disease, 150600 (3)
Osteoarthritis with mild chondrodysplasia, 604864 (3)
Platyspondylic skeletal dysplasia, Torrance type, 151210 (3)
SED congenita, 183900 (3)
SMED Strudwick type, 184250 (3)
Spondyloepiphyseal dysplasia, Stanescu type, 616583 (3)
Spondyloperipheral dysplasia, 271700 (3)
Stickler sydrome, type I, nonsyndromic ocular, 609508 (3)
Stickler syndrome, type I, 108300 (3)
Vitreoretinopathy with phalangeal epiphyseal dysplasia (3)
Achondrogenesis, type II or hypochondrogenesis, 200610 (3)
KERA Cornea plana 2, autosomal recessive, 217300 (3)
KRT3 Meesmann corneal dystrophy, 122100 (3)

Genes at Clinical Genomics Database

COL2A1, KERA, KRT3,
COL2A1 Otospondylomegaepiphyseal dysplasia
Stickler syndrome, type I
Rhegmatogenous retinal detachment, autosomal dominant
Czech dysplasia
Epiphyseal dysplasia, multiple, with myopia and deafness
Avascular necrosis of femoral head, primary
KERA Cornea plana 2, autosomal recessive
KRT3 Meesmann corneal dystrophy

Genes at HGMD

Summary

Number of Variants: 23
Number of Genes: 4

Export to: CSV
  • Page 1 of 1

COL2A1
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 12078_s17 12 rs3803183
dbSNP Clinvar 		48398080 100.0 T A PASS 0/1 21 NON_SYNONYMOUS_CODING MODERATE None 0.68530 0.68530 0.21085 0.18 0.00 None None None None None None COL2A1|0.956600158|2.04%
View 12078_s17 12 rs1635553
dbSNP Clinvar 		48375568 100.0 A G PASS 0/1 41 SYNONYMOUS_CODING LOW None 0.48283 0.48280 0.45279 None None None None None None COL2A1|0.956600158|2.04%
View 12078_s17 12 rs2276454
dbSNP Clinvar 		48376291 100.0 G A PASS 0/1 44 SYNONYMOUS_CODING LOW None 0.42971 0.42970 0.38682 None None None None None None COL2A1|0.956600158|2.04%
View 12078_s17 12 rs2070739
dbSNP Clinvar 		48367976 100.0 C T PASS 0/1 132 NON_SYNONYMOUS_CODING MODERATE None 0.17093 0.17090 0.06981 0.05 1.00 None None None None None None COL2A1|0.956600158|2.04%

KERA
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 12078_s17 12 rs2735333
dbSNP Clinvar 		91449990 100.0 C T PASS 1/1 73 SYNONYMOUS_CODING LOW None 0.62001 0.62000 0.36689 None None None None None None KERA|0.287600325|28.54%

KRT3
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 12078_s17 12 rs4432093
dbSNP Clinvar 		53186122 100.0 G A PASS 1/1 59 SYNONYMOUS_CODING LOW None 0.78774 0.78770 0.18937 None None None None None None KRT3|0.041114774|65.41%

PXN
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 12078_s17 12 rs4767884
dbSNP Clinvar 		120661977 100.0 T C PASS 1/1 149 NON_SYNONYMOUS_CODING MODERATE None 0.90076 0.90080 0.16978 0.56 0.00 None None None None None None PXN|0.716901595|8.07%
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 12078_s17 12 rs1635550
dbSNP Clinvar 		48377970 100.0 A G PASS 0/1 60 None None None 0.68311 0.68310 0.23404 None None None None None None COL2A1|0.956600158|2.04%
View 12078_s17 12 rs11168337
dbSNP Clinvar 		48376530 100.0 C A PASS 0/1 134 None None None 0.50160 0.50160 None None None None None None COL2A1|0.956600158|2.04%
View 12078_s17 12 rs3829736
dbSNP Clinvar 		48376503 100.0 C T PASS 0/1 134 None None None 0.45567 0.45570 None None None None None None COL2A1|0.956600158|2.04%
View 12078_s17 12 rs3829737
dbSNP Clinvar 		48376447 100.0 A G PASS 0/1 133 None None None None None None None None None COL2A1|0.956600158|2.04%
View 12078_s17 12 rs3842680,rs397934282
dbSNP Clinvar 		48376443 100.0 A AC PASS 0/1 175 None None None 0.43530 None None None None None None COL2A1|0.956600158|2.04%
View 12078_s17 12 rs2276456
dbSNP Clinvar 		48375975 100.0 A G PASS 0/1 60 None None None 0.47324 0.47320 0.42142 None None None None None None COL2A1|0.956600158|2.04%
View 12078_s17 12 rs2276457
dbSNP Clinvar 		48375965 100.0 C T PASS 0/1 60 None None None 0.44629 0.44630 0.38997 None None None None None None COL2A1|0.956600158|2.04%
View 12078_s17 12 rs2276458
dbSNP Clinvar 		48374826 100.0 T G PASS 0/1 73 None None None 0.31989 0.31990 0.34544 None None None None None None COL2A1|0.956600158|2.04%
View 12078_s17 12 rs1635554
dbSNP Clinvar 		48374513 100.0 A G PASS 1/1 85 None None None 0.93530 0.93530 None None None None None None COL2A1|0.956600158|2.04%
View 12078_s17 12 rs1635560
dbSNP Clinvar 		48367829 100.0 G A PASS 0/1 68 None None None 0.22304 0.22300 0.22997 None None None None None None COL2A1|0.956600158|2.04%
View 12078_s17 12 rs376000587
dbSNP Clinvar 		53187804 100.0 A T PASS 0/1 44 None None None 0.00080 0.00080 None None None None None None KRT3|0.041114774|65.41%
View 12078_s17 12 rs3803182
dbSNP Clinvar 		48398223 100.0 G A PASS 0/1 21 None None None 0.72764 0.72760 None None None None None None COL2A1|0.956600158|2.04%
View 12078_s17 12 rs3803184
dbSNP Clinvar 		48398002 100.0 G C PASS 0/1 55 None None None 0.68590 0.68590 0.21576 None None None None None None COL2A1|0.956600158|2.04%
View 12078_s17 12 rs1034762
dbSNP Clinvar 		48389643 100.0 A C PASS 0/1 84 None None None 0.68271 0.68270 0.17915 None None None None None None COL2A1|0.956600158|2.04%
View 12078_s17 12 rs1635544
dbSNP Clinvar 		48380031 100.0 A G PASS 0/1 32 None None None 0.48602 0.48600 None None None None None None COL2A1|0.956600158|2.04%
View 12078_s17 12 rs7963636
dbSNP Clinvar 		48379856 100.0 T C PASS 0/1 37 None None None 0.51198 0.51200 None None None None None None COL2A1|0.956600158|2.04%
  • Page 1 of 1