Other congenital malformations of spinal cord

Q17_OTHER_CONGEN_MALFO_SPINAL_CORD

No definition available.

Endpoint definition

↥

Report an error or suggest an improvement for this endpoint codes

Endpoint definition steps	FinnGen
Phenotype data	520210
1. Apply sex-specific rule None	520210
2. Check conditions None	520210
3. Check pre-conditions, main-only, mode, registry filters Registry filters: Hospital discharge: ICD-10 — Q06 Cause of death: ICD-10 — Q06 2 out of 7 registries used, show all original rules.	51
4. Check minimum number of events None	51
5. Include endpoints None	51
6. Filter based on genotype QC (FinnGen only)	51

Control definitions (FinnGen only)

Control exclude: Q17_CONGEN_MALFO_NERVOUS_SYSTEM

Extra metadata

Level in the ICD hierarchy: 3
First used in FinnGen datafreeze: DF4
Parent code in ICD-10: Q0
Name in latin: Aliae malformationes congenitae medullae spinalis

NAME	Q17_OTHER_CONGEN_MALFO_SPINAL_CORD
CONTROL_EXCLUDE	Q17_CONGEN_MALFO_NERVOUS_SYSTEM
CONTROL_PRECONDITIONS
CONTROL_CONDITIONS
SEX
INCLUDE
PRE_CONDITIONS
CONDITIONS
OUTPAT_ICD
OUTPAT_OPER
HD_MAINONLY
HD_ICD_10_ATC
HD_ICD_10	Q06
HD_ICD_9
HD_ICD_8
HD_ICD_10_EXCL
HD_ICD_9_EXCL
HD_ICD_8_EXCL
COD_MAINONLY
COD_ICD_10	Q06
COD_ICD_9
COD_ICD_8
COD_ICD_10_EXCL
COD_ICD_9_EXCL
COD_ICD_8_EXCL
OPER_NOM
OPER_HL
OPER_HP1
OPER_HP2
KELA_REIMB
KELA_REIMB_ICD
KELA_ATC_NEEDOTHER
KELA_ATC
KELA_VNRO_NEEDOTHER
KELA_VNRO
CANC_TOPO
CANC_TOPO_EXCL
CANC_MORPH
CANC_MORPH_EXCL
CANC_BEHAV

Similar endpoints

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List of similar endpoints to Other congenital malformations of spinal cord based on the number of shared cases.

Similar with more cases:

Similar with less cases:

None

Case counts by codes

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FinnGen case counts by registry codes:

Upset plot

Full data table

Summary Statistics

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-FinRegistry-

Key figures

	All	Female	Male
Number of individuals
Whole population	561	319	242
Only index persons	443	266	177
Unadjusted period prevalence (%)
Whole population	0.01	0.01	0.01
Only index persons	0.01	0.01	0.01
Median age at first event (years)
Whole population	-	14.91	10.34
Only index persons	22.35	26.14	16.64

-FinnGen-

Key figures

	All	Female	Male
Number of individuals	51	32	19
Unadjusted period prevalence (%)	0.01	0.01	0.01
Median age at first event (years)	45.15	46.58	42.74

-FinRegistry-

Age distribution of first events

-FinnGen-

Age distribution of first events

-FinRegistry-

Year distribution of first events

-FinnGen-

Year distribution of first events

-FinRegistry-

Cumulative Incidence Function

-FinnGen-

Cumulative Incidence Function

Not a core endpoint, no data to show.

CodeWAS (R11)

↥

CodeWAS is a tool for exploring the associations between an endpoint and all of the medical codes and drug codes.

This is a new tool, please reach out using the contact form for feedback and improvement ideas.

First, a cohort is built by matching controls to the endpoint cases using year of birth and sex. Then, a Fisher test is done for all the medical codes and drug codes between the cases and controls of this cohort. Codes are reported in the table below if they have −log₁₀(p-value) ≥ 6.

No data available

LabWAS

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N Cases

N Controls

-log₁₀(p)

cases

controls

cases

controls

unit

-log₁₀(p)

N cases

N controls

(3044640) Blood type and Crossmatch panel - Blood

126

4.02

5.65

2.7

2.3

—

(46236098) ABO and Rh group [Type] in Blood by Confirmatory method

4.04

5.58

2.4

—

(3001079) Blood group antibody screen [Presence] in Serum or Plasma

199

3.13

3.62

4.9

3.7

—

(40771025) 25-Hydroxyvitamin D3+25-Hydroxyvitamin D2 [Moles/volume] in Serum or Plasma

178

2.66

2.89

2.4

2.7

79.98

75.78

nmol/l

0.38

161

(43054903) Holo-transcobalamin II [Moles/volume] in Serum

132

2.55

2.65

1.5

1.7

100.34

96.02

pmol/l

—

(40762366) Oxygen capacity [Volume Fraction] in Arterial blood

6.01

2.62

15.7

6.5

—

(3033658) Prothrombin time (PT) actual/Normal

101

2.61

2.62

3.8

4.8

96.95

90.29

0.73

101

(3014007) Fractional oxyhemoglobin in Arterial blood

5.07

2.34

7.7

8.6

95.50

94.65

—

(3021960) Folate [Moles/volume] in Serum or Plasma

2.53

2.20

1.3

25.75

23.72

nmol/l

0.15

(3022621) pH of Urine by Test strip

3.60

2.20

7.3

1.9

—

(3023368) Bacteria identified in Blood by Culture

2.49

2.14

8.6

4.5

—

(36304419) Bacteria [Presence] in Urine

113

2.27

1.98

10.9

3.5

—

(3044889) 12 lead EKG panel

263

2.25

1.84

3.1

3.2

—

(3011397) Hemoglobin [Presence] in Urine by Test strip

108

2.21

1.83

6.8

3.5

—

(3026910) Gamma glutamyl transferase [Enzymatic activity/volume] in Serum or Plasma

304

0.47

1.78

3.7

3.1

29.43

40.11

u/l

1.07

296

(3003694) ABO and Rh group [Type] in Blood

143

2.11

1.77

1.2

1.5

—

(36031861) Influenza virus A and B and SARS-CoV-2 (COVID-19) and Respiratory syncytial virus RNA panel - Respiratory system specimen by NAA with probe detection

4.14

1.76

2.2

2.4

—

(3006217) Methemoglobin/Hemoglobin.total in Arterial blood

3.84

1.65

8.2

7.7

0.70

0.87

—

(3029287) Urinalysis microscopic panel [#/volume] - Urine by Automated count

139

2.02

1.59

10.5

3.9

—

(3004119) Hemoglobin [Mass/volume] in Venous blood

3.34

1.47

29.2

4.7

116.80

133.56

g/l

—

(3026008) Bacteria identified in Urine by Culture

117

1.99

1.45

11.2

2.5

—

(3042936) Bacteria identified in Isolate by Culture

2.35

1.38

5.0

2.0

—

(3045414) Leukocytes [Presence] in Urine

2.96

1.31

1.8

1.3

—

(3000330) Specific gravity of Urine by Test strip

2.80

1.24

2.4

2.1

—

(3051552) Clostridioides difficile toxin genes [Presence] in Stool by NAA with probe detection

2.66

1.18

7.2

1.5

—

(3019060) Gas panel - Arterial blood

2.66

1.18

15.6

5.3

—

(3037467) Urinalysis macro (dipstick) panel - Urine

287

1.86

1.17

10.8

3.9

—

(3015399) Transferrin receptor.soluble [Mass/volume] in Serum or Plasma

1.95

1.16

2.7

2.0

1.88

2.89

mg/l

1.60

(3016293) Bicarbonate [Moles/volume] in Serum or Plasma

2.16

1.04

32.1

7.8

25.57

25.46

mmol/l

—

(3022948) Iron [Moles/volume] in Serum or Plasma

2.02

1.00

2.7

2.8

7.39

15.94

umol/l

—

(3015736) pH of Urine

158

1.69

0.97

4.7

3.5

—

(3012544) pH of Venous blood

1.97

0.91

23.8

6.8

—

(1761868) Lipid panel - Serum or Plasma

135

0.52

0.89

1.3

2.2

—

(3001784) Prostate Specific Ag Free/Prostate specific Ag.total in Serum or Plasma

1.85

0.87

3.0

5.5

24.12

23.11

—

(3007853) Bacteria identified in Skin by Aerobe culture

1.88

0.82

6.8

1.6

—

(3043924) Respiratory syncytial virus RNA [Identifier] in Specimen by NAA with probe detection

1.97

0.77

3.4

2.2

—

(3038288) Influenza virus B RNA [Presence] in Specimen by NAA with probe detection

1.92

0.76

4.3

2.2

—

(3013603) Prostate specific Ag [Mass/volume] in Serum or Plasma

1.66

0.72

2.5

5.2

2.02

2.03

ug/l

0.00

(40768797) Stomach Pathology biopsy report

1.73

0.70

1.0

1.2

—

(40761535) Cells panel - Urine sediment

1.80

0.65

3.8

4.1

—

(3002256) Pathology report gross observation

1.64

0.63

1.4

1.1

—

(3019902) Methicillin resistant Staphylococcus aureus [Presence] in Specimen by Organism specific culture

1.74

0.63

2.4

4.1

—

(3003327) Ova and parasites identified in Stool by Light microscopy

0.00

0.61

0.0

1.5

—

(3027944) Amphetamines [Presence] in Urine

0.00

0.61

0.0

1.3

—

(3020961) Endomysium IgA Ab [Titer] in Serum

0.00

0.60

0.0

1.3

—

(3013512) EKG study

108

0.59

0.56

1.3

3.4

—

(3013707) Erythrocyte sedimentation rate by Westergren method

332

0.71

0.51

5.1

4.1

11.62

10.42

mm/h

0.18

310

(3000494) Fungus identified in Specimen by Culture

1.46

0.47

3.1

1.5

—

(43054914) Glucose tolerance 2 hours panel - Serum or Plasma

1.46

0.47

3.1

2.1

—

(3001122) Ferritin [Mass/volume] in Serum or Plasma

190

1.38

0.47

3.3

2.7

69.96

85.41

ug/l

0.45

180

(3044938) Influenza virus A RNA [Presence] in Specimen by NAA with probe detection

1.54

0.46

3.9

2.4

—

(3041096) Erythrocytes [Presence] in Urine by Automated

101

0.64

0.45

5.1

3.0

—

(3022313) Gas panel - Capillary blood

1.68

0.44

38.4

6.9

—

(46235355) HIV 1 and 2 tests - Meaningful Use set

110

0.68

0.43

2.6

1.9

—

(21492888) Glucose tolerance 2 hours gestational panel - Serum or Plasma

0.00

0.42

0.0

1.5

—

(3050380) Cytology report of Cervical or vaginal smear or scraping Cyto stain

0.00

0.42

0.0

1.3

—

(4034850)

0.00

0.42

0.0

6.4

—

(3000991) Gas panel - Venous blood

1.45

0.36

12.0

7.9

—

(3009542) Hematocrit [Volume Fraction] of Blood

416

1.42

0.25

31.6

13.2

37.49

39.97

0.68

336

(3021879) Hepatitis B virus core Ab [Presence] in Serum

1.39

0.24

1.2

1.6

—

(40760892) CBC W Ordered Manual Differential panel - Blood

1.30

0.23

3.8

4.9

—

(3006093) Chlamydia trachomatis DNA [Presence] in Specimen by NAA with probe detection

1.28

0.23

1.6

2.0

—

(3022250) Lactate dehydrogenase [Enzymatic activity/volume] in Serum or Plasma by Lactate to pyruvate reaction

1.21

0.22

1.4

5.1

234.40

236.76

u/l

—

(3028286) Albumin [Mass/volume] in Serum or Plasma by Electrophoresis

0.00

0.21

0.0

1.0

—

38.25

—

(3029379) Protein.monoclonal band 4 [Mass/volume] in Serum or Plasma by Electrophoresis

0.00

0.21

0.0

1.0

—

0.00

—

(3023420) DNA double strand Ab [Units/volume] in Serum

0.00

0.21

0.0

1.4

—

(3029338) Protein.monoclonal band 3 [Mass/volume] in Serum or Plasma by Electrophoresis

0.00

0.21

0.0

1.0

—

0.00

—

(40765161) Human bocavirus DNA [Presence] in Specimen by NAA with probe detection

0.00

0.21

0.0

2.7

—

(3027315) Oxygen [Partial pressure] in Blood

0.00

0.21

0.0

4.5

—

8.60

—

(3013290) Carbon dioxide [Partial pressure] in Blood

0.00

0.21

0.0

4.5

—

5.17

—

(44816559) Phosphatidylethanol [Mass/volume] in Blood

0.00

0.21

0.0

1.2

—

(3029713) Protein.monoclonal band 1 [Mass/volume] in Serum or Plasma by Electrophoresis

0.00

0.21

0.0

1.2

—

1.21

—

(3035797) Protein.monoclonal band 2 [Mass/volume] in Serum or Plasma by Electrophoresis

0.00

0.21

0.0

1.2

—

0.00

—

(3023465) Gamma globulin [Mass/volume] in Serum or Plasma by Electrophoresis

0.00

0.21

0.0

1.0

—

9.84

—

(3043723) Beta 1 globulin [Mass/volume] in Serum or Plasma by Electrophoresis

0.00

0.21

0.0

1.2

—

(3043109) Cytology report of Tissue fine needle aspirate Cyto stain

0.00

0.21

0.0

1.1

—

(40764999) Glomerular filtration rate/1.73 sq M.predicted [Volume Rate/Area] in Serum, Plasma or Blood by Creatinine-based formula (CKD-EPI)

372

0.81

0.21

10.6

11.0

89.82

86.99

ml/min/173m2

0.25

301

(1002102) Choriogonadotropin.intact+Beta subunit [Mass/volume] in Serum or Plasma

0.00

0.20

0.0

1.3

—

(3023511) Choriogonadotropin [Units/volume] in Urine

0.00

0.20

0.0

1.5

—

(40763086) Leukocyte esterase [Presence] in Urine by Automated test strip

148

1.22

0.20

6.6

3.4

—

(3024135) Streptococcus.beta-hemolytic [Presence] in Throat by Organism specific culture

108

0.80

0.14

3.0

1.7

—

(21494755) Public health laboratory ask at order entry panel

1.18

0.10

1.2

—

(706163) SARS-CoV-2 (COVID-19) RNA [Presence] in Respiratory system specimen by NAA with probe detection

325

0.88

0.10

3.6

3.4

—

(3006923) Alanine aminotransferase [Enzymatic activity/volume] in Serum or Plasma

466

0.87

0.10

10.8

9.9

28.33

26.36

u/l

0.22

454

(3045783) Sodium and Potassium panel [Moles/volume] - Serum or Plasma

1.15

0.10

5.0

5.2

—

(3024950) Chlamydia trachomatis DNA [Presence] in Urine by NAA with probe detection

0.77

0.09

1.8

2.3

—

(3037522) Nuclear Ab [Titer] in Serum

1.13

0.08

1.1

1.4

—

590.00

—

(3018006) Microscopic observation [Identifier] in Cervix by Cyto stain.thin prep

0.82

0.08

1.7

1.3

—

(40758558) Short blood count panel - Blood

127

0.93

0.02

5.3

9.0

—

(40768804) Tissue Pathology biopsy report

147

0.93

0.02

3.0

1.9

—

(3007220) Creatine kinase [Enzymatic activity/volume] in Serum or Plasma

106

1.05

0.00

2.0

2.4

171.09

123.89

u/l

0.29

101

(42870588) Differential panel, method unspecified - Blood

156

1.04

0.00

7.1

6.6

—

(3004383) Neutrophil cytoplasmic Ab.classic [Titer] in Serum by Immunofluorescence

0.00

0.0

1.0

—

(3042596) Human coronavirus RNA [Presence] in Specimen by NAA with probe detection

0.00

0.0

2.8

—

(40759843) Sjogrens syndrome-A extractable nuclear Ab [Presence] in Serum by Immunoblot

0.00

0.0

1.0

—

(3035933) Granulocytes/100 leukocytes in Blood

0.00

0.0

1.0

—

(40759836) Histone Ab [Presence] in Serum by Immunoblot

0.00

0.0

1.0

—

(42529215) Follitropin [Units/volume] in Serum or Plasma by Immunoassay

0.00

0.0

1.5

—

33.78

—

(3040359) Human coronavirus NL63 RNA [Presence] in Specimen by NAA with probe detection

0.00

0.0

2.2

—

(40759812) SCL-70 extractable nuclear Ab [Presence] in Serum by Immunoblot

0.00

0.0

1.0

—

(40768795) Lymph node Pathology biopsy report

0.00

0.0

1.2

—

(3012220) Varicella zoster virus IgM Ab [Presence] in Serum by Immunoassay

0.00

0.0

1.3

—

(3051611) Lipemic interference index of Serum or Plasma

0.00

0.0

3.3

—

(36033641) SARS-CoV-2 (COVID-19) Ag [Presence] in Upper respiratory specimen by Rapid immunoassay

0.00

0.0

1.4

—

(3049539) Genetic diseases [Identifier] in Blood or Tissue by FISH Nominal

0.00

0.0

1.2

—

(3044927) Protein electrophoresis panel - Urine

0.00

0.0

1.0

—

(1617658) Protocol used for examination of sentinel lymph nodes

0.00

0.0

1.0

—

(1616796) Gas panel - Central venous blood

0.00

0.0

3.1

—

(36660697) Celiac disease serology panel - Serum

0.94

0.00

1.0

1.2

—

(3045142) Bone marrow Pathology biopsy report

0.00

0.0

1.3

—

(3004616) Nuclear Ab [Presence] in Serum

0.00

0.0

1.1

—

(3021901) Oxygen saturation in Capillary blood

0.00

0.0

9.1

—

(40759849) Smith extractable nuclear Ab [Presence] in Serum by Immunoblot

0.00

0.0

1.0

—

(40759844) Sjogrens syndrome-B extractable nuclear Ab [Presence] in Serum by Immunoblot

0.00

0.0

1.0

—

(3019284) Hepatitis B virus surface Ag [Presence] in Serum

0.92

0.00

1.9

1.7

—

(3000093) Morphology [Interpretation] in Blood Narrative

0.00

0.0

1.0

—

(3008757) Leukocyte morphology finding [Identifier] in Blood

0.00

0.0

7.0

—

(40769539) Bacteria identified based on 16S rRNA gene [Identifier] in Specimen by Sequencing

0.00

0.0

1.3

—

(3031478) Chlamydophila pneumoniae DNA [Presence] in Specimen by NAA with probe detection

0.00

0.0

2.2

—

(3006588) Cancer Ag 15-3 [Units/volume] in Serum or Plasma

0.00

0.0

4.0

—

14.67

—

(3016650) Hepatitis A virus Ab [Presence] in Serum

0.00

0.0

1.0

—

(3022806) Fractional oxyhemoglobin in Capillary blood

0.00

0.0

3.1

—

90.74

—

(3028271) Lactate [Moles/volume] in Capillary blood

0.00

0.0

3.6

—

1.54

—

(3036086) Jo-1 extractable nuclear Ab [Units/volume] in Serum by Immunoassay

0.00

0.0

1.6

—

(3019539) Treponema pallidum Ab [Titer] in Serum by Hemagglutination

0.00

0.0

1.5

—

(3042631) Mycobacterium sp identified in Specimen

0.00

0.0

6.2

—

(3050238) Crystals [Presence] in Synovial fluid by Light microscopy

0.00

0.0

1.0

—

(3021125) Hepatitis C virus RNA [Presence] in Serum or Plasma by NAA with probe detection

0.00

0.0

1.7

—

(3007566) Smooth muscle Ab [Titer] in Serum

0.00

0.0

1.0

—

(3014148) Varicella zoster virus Ab [Titer] in Serum

0.00

0.0

1.4

—

(3037756) Immunofixation for Serum or Plasma

0.00

0.0

1.3

—

(3021952) Alkaline phosphatase isoenzymes [Enzymatic activity/volume] in Serum or Plasma by Heat stability

0.00

0.0

1.1

—

(3000855) Microscopic observation [Identifier] in Vaginal fluid by Gram stain

0.00

0.0

1.2

—

(3041642) Human coronavirus 229E RNA [Presence] in Specimen by NAA with probe detection

0.00

0.0

2.2

—

(3033319) Streptococcus pyogenes Ag [Presence] in Throat

0.87

0.00

2.2

1.8

—

(3029080) Hemoglobin [Entitic mass] in Reticulocytes

0.00

0.0

1.2

—

31.40

—

(3051651) Icteric interference index of Serum or Plasma

0.00

0.0

3.3

—

(3017143) Hepatitis C virus Ab [Presence] in Serum

0.96

0.00

1.7

1.6

—

(3005136) Cladosporium herbarum IgE Ab [Units/volume] in Serum

0.00

0.0

1.0

—

(3038546) Human coronavirus OC43 RNA [Presence] in Specimen by NAA with probe detection

0.00

0.0

2.2

—

(44816844) Macroprolactin [Units/volume] in Serum or Plasma

0.00

0.0

1.3

—

(3025018) Bordetella pertussis Ab [Titer] in Serum

0.00

0.0

1.0

—

(40759842) Ribonucleoprotein extractable nuclear Ab [Presence] in Serum by Immunoblot

0.00

0.0

1.0

—

(3034770) Mitochondria Ab [Titer] in Serum

0.00

0.0

1.0

—

(4094501)

0.00

0.0

1.2

—

(3021236) Streptolysin O Ab [Units/volume] in Serum or Plasma

0.00

0.0

1.2

—

93.88

—

(3048821) Cortisol [Moles/volume] in Serum or Plasma --post 1 mg dexamethasone PO overnight

0.00

0.0

1.1

—

Mortality – FinRegistry

↥

Association

Association between endpoint Q17_OTHER_CONGEN_MALFO_SPINAL_CORD and mortality.

Females

No data

Males

No data

Mortality risk

Mortality risk for people of age

years, who have Q17_OTHER_CONGEN_MALFO_SPINAL_CORD.

N-year risk	Females	Males
1	No data	No data
5	No data	No data
10	No data	No data
15	No data	No data
20	No data	No data

Relationships between endpoints

↥

Index endpoint: Q17_OTHER_CONGEN_MALFO_SPINAL_CORD – Other congenital malformations of spinal cord

GWS hits: -

Endpoint

Case Overlap

Survival Analysis

Genetic Correlations

Genetic Signals

N (Jaccard index)

HR [CI]

rg [CI]

Hits

Coloc Hits

FinRegistry

FinnGen

FinRegistry

FinnGen

Loading data

Other congenital malformations of spinal cord

Endpoint definition

Endpoint definition steps

FinnGen

Phenotype data

1. Apply sex-specific rule

2. Check conditions

3. Check pre-conditions, main-only, mode, registry filters

4. Check minimum number of events

5. Include endpoints

6. Filter based on genotype QC (FinnGen only)

Similar endpoints

Case counts by codes

Summary Statistics

-FinRegistry-

Key figures

-FinnGen-

Key figures

-FinRegistry-

Age distribution of first events

-FinnGen-

Age distribution of first events

-FinRegistry-

Year distribution of first events

-FinnGen-

Year distribution of first events

-FinRegistry-

Cumulative Incidence Function

-FinnGen-

Cumulative Incidence Function

CodeWAS (R11)

LabWAS

Mortality – FinRegistry

Association

Females

Males

Mortality risk

Relationships between endpoints