Severe combined immunodeficiency [SCID] with low or normal B-cell numbers

D3_SCIDC

No definition available.

Endpoint definition

↥

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 — D81.2 Cause of death: ICD-10 — D81.2 2 out of 7 registries used, show all original rules.	22
4. Check minimum number of events None	22
5. Include endpoints None	22
6. Filter based on genotype QC (FinnGen only)	22

Control definitions (FinnGen only)

Control exclude: D3_IMMUNEMECHANISM

Extra metadata

Level in the ICD hierarchy: 4
First used in FinnGen datafreeze: DF2
Parent code in ICD-10: D81
Name in latin: Deficientia immunalis mixta gravis cum deficientia sive numero normali cellularum B

NAME	D3_SCIDC
CONTROL_EXCLUDE	D3_IMMUNEMECHANISM
CONTROL_PRECONDITIONS
CONTROL_CONDITIONS
SEX
INCLUDE
PRE_CONDITIONS
CONDITIONS
OUTPAT_ICD
OUTPAT_OPER
HD_MAINONLY
HD_ICD_10_ATC
HD_ICD_10	D812
HD_ICD_9	$!$	The FinnGen clinical team has checked and no code can be used for this rule.
HD_ICD_8	$!$	The FinnGen clinical team has checked and no code can be used for this rule.
HD_ICD_10_EXCL
HD_ICD_9_EXCL
HD_ICD_8_EXCL
COD_MAINONLY
COD_ICD_10	D812
COD_ICD_9	$!$	The FinnGen clinical team has checked and no code can be used for this rule.
COD_ICD_8	$!$	The FinnGen clinical team has checked and no code can be used for this rule.
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

↥

List of similar endpoints to Severe combined immunodeficiency [SCID] with low or normal B-cell numbers based on the number of shared cases.

Similar with more cases:

Similar with less cases:

None

Case counts by codes

↥

FinnGen case counts by registry codes:

Upset plot

Full data table

Summary Statistics

↥

-FinRegistry-

Key figures

	All	Female	Male
Number of individuals
Whole population	194	144	49
Only index persons	163	130	33
Unadjusted period prevalence (%)
Whole population	0.00	0.00	0.00
Only index persons	0.00	0.00	0.00
Median age at first event (years)
Whole population	56.05	54.27	61.68
Only index persons	54.39	52.61	61.43

-FinnGen-

Key figures

	All	Female	Male
Number of individuals	22	18	-
Unadjusted period prevalence (%)	0.01	0.01	-
Median age at first event (years)	52.22	49.70	-

-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

No data

-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

↥

(ID) Name

N Cases

N Controls

-log₁₀(p)

cases

controls

cases

controls

unit

-log₁₀(p)

N cases

N controls

(3048773) Triglyceride [Moles/volume] in Serum or Plasma --fasting

185

0.33

1.46

4.4

4.3

1.2

1.3

mmol/l

0.24

169

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

2.33

1.16

1.7

2.1

93.1

91.7

pmol/l

—

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

2.29

1.13

1.1

1.6

19.8

29.0

nmol/l

—

(40761511) CBC panel - Blood by Automated count

193

0.38

1.03

12.2

14.3

—

(3001308) Cholesterol in LDL [Moles/volume] in Serum or Plasma

192

0.39

1.01

6.3

5.2

2.7

mmol/l

0.02

178

(3019900) Cholesterol [Moles/volume] in Serum or Plasma

189

0.44

0.93

4.8

4.7

4.6

mmol/l

0.21

175

(3023602) Cholesterol in HDL [Moles/volume] in Serum or Plasma

187

0.47

0.86

4.6

4.8

1.5

mmol/l

0.10

171

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

0.00

0.85

0.0

9.0

—

(42870588) Differential panel, method unspecified - Blood

1.80

0.66

7.7

4.8

—

(3009201) Thyrotropin [Units/volume] in Serum or Plasma

185

0.51

0.64

6.0

5.5

1.4

2.0

mu/l

2.38

169

(3016771) Amylase [Enzymatic activity/volume] in Serum or Plasma

1.61

0.47

3.7

2.5

143.1

55.5

u/l

—

(3004410) Hemoglobin A1c/Hemoglobin.total in Blood

188

0.58

0.46

6.2

38.4

40.0

mmol/mol

0.49

175

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

0.63

0.43

2.7

3.8

—

(40761536) Microorganisms panel - Urine sediment

0.00

0.43

0.0

4.1

—

(3017732) Neutrophils [#/volume] in Blood

0.00

0.43

0.0

1.9

—

3.9

—

(40761535) Cells panel - Urine sediment

0.00

0.42

0.0

5.8

—

(46236952) Glomerular filtration rate/1.73 sq M.predicted [Volume Rate/Area] in Serum, Plasma or Blood by Creatinine-based formula (MDRD)

0.00

0.42

0.0

2.9

—

59.7

—

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

0.00

0.42

0.0

6.4

—

(3032080) INR in Blood by Coagulation assay

0.68

0.31

21.8

10.3

—

1.3

—

(3037467) Urinalysis macro (dipstick) panel - Urine

128

1.54

0.30

4.3

4.6

—

(3019150) Specific gravity of Urine by Refractometry

1.36

0.25

2.2

5.0

—

1.0

—

(3026782) Osmolality of Urine

1.32

0.24

4.0

2.8

590.8

491.5

mosm/kgh2o

—

(3000850) Epithelial cells [#/volume] in Urine

1.28

0.24

4.2

2.8

1.7

4.6

e6/l

—

(3006504) Eosinophils/100 leukocytes in Blood

101

1.41

0.23

7.6

5.7

2.8

2.4

0.51

(3033658) Prothrombin time (PT) actual/Normal

1.34

0.23

2.3

3.7

109.3

91.2

—

(3051714) Fibrin D-dimer FEU [Mass/volume] in Platelet poor plasma

1.34

0.23

1.5

2.1

1.1

1.0

mg/l

—

(40760892) CBC W Ordered Manual Differential panel - Blood

1.31

0.22

1.3

6.9

—

(46235759) Influenza virus B RNA [Presence] in Nasopharynx by NAA with probe detection

0.00

0.22

0.0

2.6

—

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

0.00

0.22

0.0

1.3

—

(3014007) Fractional oxyhemoglobin in Arterial blood

0.00

0.22

0.0

4.6

—

91.8

—

(3003510) Neisseria gonorrhoeae DNA [Presence] in Urine by NAA with probe detection

0.00

0.22

0.0

1.2

—

(3004716) Salmonella sp identified in Stool by Organism specific culture

0.00

0.22

0.0

1.4

—

(21494755) Public health laboratory ask at order entry panel

0.00

0.22

0.0

1.1

—

(3018010) Neutrophils/100 leukocytes in Blood

102

1.39

0.21

7.6

5.4

53.6

56.0

0.27

(3025941) Bacteria identified in Stool by Culture

0.00

0.21

0.0

1.2

—

(40768443) Skin Pathology biopsy report

0.00

0.21

0.0

1.3

—

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

0.00

0.21

0.0

1.5

—

(3044640) Blood type and Crossmatch panel - Blood

0.72

0.20

1.6

2.2

—

(3026008) Bacteria identified in Urine by Culture

0.73

0.20

2.0

3.1

—

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

0.73

0.19

2.8

4.9

—

(3019069) Monocytes/100 leukocytes in Blood

103

1.36

0.19

7.8

5.9

8.1

8.7

0.34

(3002030) Lymphocytes/100 leukocytes in Blood

103

1.36

0.19

7.6

5.8

32.3

29.2

0.47

(3015736) pH of Urine

0.76

0.19

2.8

4.3

—

(40768804) Tissue Pathology biopsy report

0.74

0.19

3.4

2.0

—

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

115

1.32

0.18

2.1

2.6

—

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

1.32

0.16

1.9

2.6

161.9

91.6

ug/l

—

(3041096) Erythrocytes [Presence] in Urine by Automated

1.12

0.10

2.8

4.3

—

(3013707) Erythrocyte sedimentation rate by Westergren method

159

0.82

0.09

4.9

4.4

14.8

12.4

mm/h

0.29

147

(3008486) Thyroxine (T4) free [Moles/volume] in Serum or Plasma

159

0.82

0.09

4.4

4.6

14.6

15.2

pmol/l

0.86

142

(3003338) MCHC [Mass/volume]

146

0.89

0.09

20.9

20.5

327.3

331.4

g/l

0.72

146

(3015377) Calcium [Moles/volume] in Serum or Plasma

0.82

0.09

8.6

3.3

2.4

mmol/l

—

(3022096) Basophils/100 leukocytes in Blood

1.22

0.08

8.0

5.6

0.7

0.06

(3013826) Glucose [Moles/volume] in Serum or Plasma

109

1.22

0.08

6.3

5.5

6.1

6.6

mmol/l

0.91

101

(3044889) 12 lead EKG panel

130

0.83

0.07

3.2

4.2

—

(3006140) Bilirubin.total [Moles/volume] in Serum or Plasma

106

0.90

0.01

7.2

8.2

10.4

umol/l

—

101

(3007628) Bicarbonate [Moles/volume] standard in Venous blood

0.00

0.0

2.7

—

25.0

—

(3027545) Mycoplasma pneumoniae Ab [Presence] in Serum by Immunoassay

0.00

0.0

1.7

—

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

0.00

0.0

7.3

—

0.0

—

(3010521) Mycoplasma pneumoniae IgM Ab [Presence] in Serum by Immunoassay

0.00

0.0

1.0

—

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

0.00

0.0

1.6

—

(3048929) Epstein Barr virus Ab [Presence] in Serum

0.00

0.0

1.4

—

(3042194) Human metapneumovirus RNA [Presence] in Specimen by NAA with probe detection

0.00

0.0

2.3

—

(40766189) Gliadin peptide IgG Ab [Units/volume] in Serum by Immunoassay

0.00

0.0

1.1

—

(3010130) Cytomegalovirus IgG Ab [Units/volume] in Serum or Plasma

0.00

0.0

1.1

—

(3015635) Cytomegalovirus IgM Ab [Units/volume] in Serum or Plasma

0.00

0.0

1.1

—

(3019832) Treponema pallidum Ab [Presence] in Serum

0.00

0.0

1.6

—

(4034850)

0.00

0.0

10.7

—

(3040853) Adenovirus DNA [Identifier] in Specimen by NAA with probe detection

0.00

0.0

2.3

—

(3029080) Hemoglobin [Entitic mass] in Reticulocytes

0.00

0.0

2.4

—

30.8

—

(3012568) Campylobacter sp identified in Specimen by Organism specific culture

0.00

0.0

1.4

—

(3044254) Respiratory syncytial virus RNA [Presence] in Specimen by NAA with probe detection

0.00

0.0

2.3

—

(1761868) Lipid panel - Serum or Plasma

0.94

0.00

2.3

3.1

—

(3020148) Glutamate decarboxylase 65 Ab [Units/volume] in Serum

0.00

0.0

1.2

—

(3002482) Mycoplasma pneumoniae DNA [Presence] in Specimen by NAA with probe detection

0.00

0.0

2.0

—

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

0.00

0.0

2.0

—

(3007844) Epstein Barr virus capsid IgM Ab [Units/volume] in Serum by Immunoassay

0.00

0.0

1.2

—

(3032035) Polymorphonuclear cells/100 leukocytes in Blood

0.00

0.0

2.0

—

51.2

—

(3024403) Complement+Immunoglobulin [Units/volume] in Red Blood Cells

0.00

0.0

1.4

—

(36304419) Bacteria [Presence] in Urine

0.88

0.00

4.0

2.9

—

(36305247) Microscopic observation [Identifier] in Isolate by Gram stain

0.00

0.0

1.8

—

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

0.00

0.0

5.3

—

25.5

—

(40758558) Short blood count panel - Blood

1.07

0.00

13.7

6.4

—

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

1.02

0.00

3.9

3.1

—

(1761482) Bacteria [#/volume] in Urine by Culture

0.00

0.0

7.4

—

(3024522) Salmonella sp identified in Specimen by Organism specific culture

0.00

0.0

1.4

—

(3012477) Bordetella pertussis DNA [Presence] in Specimen by NAA with probe detection

0.00

0.0

2.0

—

(3024561) Albumin [Mass/volume] in Serum or Plasma

0.89

0.00

7.3

4.6

36.1

36.0

g/l

—

(3035995) Alkaline phosphatase [Enzymatic activity/volume] in Serum or Plasma

163

0.93

0.00

8.2

8.5

85.4

79.8

u/l

0.23

147

(3020565) Legionella pneumophila DNA [Presence] in Specimen by NAA with probe detection

0.00

0.0

2.0

—

(3030905) Polymorphonuclear cells [#/volume] in Blood

0.00

0.0

1.6

—

6.2

—

(3025468) Yersinia sp identified in Specimen by Organism specific culture

0.00

0.0

1.4

—

(42868716) Shigella species+EIEC invasion plasmid antigen H ipaH gene [Presence] in Stool by NAA with probe detection

0.00

0.0

1.4

—

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

0.00

-0.00

0.0

1.2

—

(3027315) Oxygen [Partial pressure] in Blood

0.00

-0.00

0.0

4.8

—

8.7

—

(3017918) Cytomegalovirus IgG Ab [Titer] in Serum or Plasma

0.00

-0.00

0.0

1.3

—

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

0.00

-0.00

0.0

2.3

—

11.8

—

(3038515) Glucose [Moles/volume] in Venous blood

0.00

-0.00

0.0

3.3

—

8.0

—

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

0.00

-0.00

0.0

1.8

—

(3014765) Yersinia sp identified in Stool by Organism specific culture

0.00

-0.00

0.0

1.7

—

(3005988) Vibrio sp identified in Specimen by Organism specific culture

0.00

-0.00

0.0

1.3

—

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

0.00

-0.00

0.0

1.0

—

(3008037) Lactate [Moles/volume] in Venous blood

0.00

-0.00

0.0

3.3

—

1.4

—

(21493466) Plesiomonas shigelloides DNA [Presence] in Stool by NAA with non-probe detection

0.00

-0.00

0.0

1.3

—

(3001019) Free T4 and TSH panel - Serum or Plasma

0.00

-0.00

0.0

1.4

—

(3030692) Respiratory virus DNA+RNA [Identifier] in Specimen by NAA with probe detection

0.00

-0.00

0.0

1.7

—

(1002224) Polysomnography panel

0.00

-0.00

0.0

1.0

—

(3008909) Norovirus RNA [Presence] in Stool by NAA with probe detection

0.00

-0.00

0.0

1.2

—

(42529406) Shigella sp [Presence] in Stool by Culture

0.00

-0.00

0.0

1.7

—

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

0.00

-0.00

0.0

2.5

—

(3024891) Influenza virus A+B Ag [Presence] in Specimen

0.00

-0.00

0.0

1.0

—

(40768793) Breast Pathology biopsy report

0.00

-0.00

0.0

1.2

—

(1616796) Gas panel - Central venous blood

0.00

-0.00

0.0

2.1

—

(36032419) SARS-CoV-2 (COVID-19) Ag [Presence] in Upper respiratory specimen by Immunoassay

0.00

-0.00

0.0

1.2

—

(3013290) Carbon dioxide [Partial pressure] in Blood

0.00

-0.00

0.0

4.8

—

4.9

—

(3006418) Campylobacter sp identified in Tissue by Organism specific culture

0.00

-0.00

0.0

1.7

—

Mortality – FinRegistry

↥

Association

Association between endpoint D3_SCIDC and mortality.

Females

No data

Males

No data

Mortality risk

Mortality risk for people of age

years, who have D3_SCIDC.

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: D3_SCIDC – Severe combined immunodeficiency [SCID] with low or normal B-cell numbers

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

Severe combined immunodeficiency [SCID] with low or normal B-cell numbers

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