Common variable immunodeficiency with predominant abnormalities of T-cell numbers and function

D3_CVID_TCELL

obsolete_common variable immunodeficiency: ['A hypogammaglobulinemia that is results in insufficient production of antibodies needed to respond to exposure of pathogens and is characterized by low Ig levels with phenotypically normal B cells that can proliferate but do not develop into Ig-producing cells. Patients with common variable immunodeficiency have marked reduction in serum levels of both immunoglobulin G (IgG) and immunoglobulin A (IgA); about half of these patients also have reduced immunoglobulin M (IgM).', 'A primary immunodeficiency characterized by low levels or absence of all the immunoglobulin classes and lack of B-lymphocytes or plasma cells. It results in recurrent bacterial infections. Complications include autoimmune phenomena and cancer development.', 'Heterogeneous group of immunodeficiency syndromes characterized by hypogammaglobulinemia of most isotypes, variable B-cell defects, and the presence of recurrent bacterial infections.']

Suggest a new description

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 — D83.1 Hospital discharge: ICD-9 — 2791X Cause of death: ICD-10 — D83.1 Cause of death: ICD-9 — 2791X 2 out of 7 registries used, show all original rules.	46
4. Check minimum number of events None	46
5. Include endpoints None	46
6. Filter based on genotype QC (FinnGen only)	46

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: D83
Name in latin: Deficientia immunalis variabilis communis praecipue cum abnormalitatibus cellularum T immunoregulatoriarum

NAME	D3_CVID_TCELL
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	D831
HD_ICD_9	2791X
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	D831
COD_ICD_9	2791X
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 Common variable immunodeficiency with predominant abnormalities of T-cell numbers and function 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	204	98	102
Only index persons	165	86	79
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	60.05	57.52	61.99
Only index persons	57.77	56.84	58.79

-FinnGen-

Key figures

	All	Female	Male
Number of individuals	46	28	18
Unadjusted period prevalence (%)	0.01	0.01	0.01
Median age at first event (years)	61.19	56.53	68.42

-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

(3004789) Transferrin [Mass/volume] in Serum or Plasma

4.55

5.48

7.0

1.7

2.1

2.5

g/l

1.19

(40763571) Iron/Transferrin [Ratio] in Serum or Plasma

4.50

5.25

8.1

1.8

23.5

21.0

0.29

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

3.98

4.48

8.5

1.7

12.0

11.7

umol/l

0.07

(3018405) Lactate [Moles/volume] in Arterial blood

8.91

3.70

3.1

3.9

1.3

1.9

mmol/l

—

(42870588) Differential panel, method unspecified - Blood

121

3.06

3.38

23.6

4.5

—

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

6.65

3.15

1.7

1.1

—

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

119

2.87

3.02

7.0

3.4

—

(36304419) Bacteria [Presence] in Urine

2.80

2.81

6.8

3.0

—

(3030467) Casts [#/volume] in Urine by Automated count

2.70

2.59

7.3

3.2

0.4

e6/l

0.02

(3000492) Spirometry study

3.88

2.55

3.2

1.4

—

(3052851) Hemolysis interference index of Serum or Plasma

5.56

2.48

2.7

3.5

—

(40768797) Stomach Pathology biopsy report

2.96

2.46

1.4

1.2

—

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

2.70

2.46

5.8

2.1

2.6

2.7

mg/l

0.17

(3022096) Basophils/100 leukocytes in Blood

159

2.46

2.27

28.0

5.2

0.7

0.13

147

(3000620) Complement C3 [Mass/volume] in Serum or Plasma

6.07

2.27

1.4

1.0

1.2

g/l

—

(3006217) Methemoglobin/Hemoglobin.total in Arterial blood

4.15

2.25

14.0

17.6

1.0

0.6

—

(3028653) Carboxyhemoglobin/Hemoglobin.total in Arterial blood

4.15

2.25

14.0

17.6

1.6

1.5

—

(40758558) Short blood count panel - Blood

2.61

2.24

25.7

7.4

—

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

2.61

2.24

4.7

3.2

—

(3006504) Eosinophils/100 leukocytes in Blood

163

2.37

2.11

28.3

5.1

2.5

0.04

151

(3030306) Epithelial cells.non-squamous [#/volume] in Urine by Automated count

2.68

2.08

4.1

2.7

1.1

0.9

e6/l

—

(3019069) Monocytes/100 leukocytes in Blood

164

2.35

2.07

28.8

5.6

10.4

8.6

1.98

152

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

156

2.32

2.02

10.4

4.9

32.6

35.6

g/l

1.62

144

(3021447) Carbon dioxide [Partial pressure] in Venous blood

3.56

1.97

7.7

3.1

5.6

6.2

kpa

—

(3002030) Lymphocytes/100 leukocytes in Blood

169

2.24

1.87

28.8

5.3

25.5

27.3

0.42

157

(3027945) Reticulocytes/100 erythrocytes in Blood

2.86

1.86

2.1

1.9

1.7

—

(3024354) Oxygen [Partial pressure] in Venous blood

3.67

1.81

3.8

2.2

3.5

4.0

kpa

—

(3014007) Fractional oxyhemoglobin in Arterial blood

3.67

1.81

16.2

18.5

92.9

94.6

—

(3012544) pH of Venous blood

3.25

1.80

7.7

3.9

—

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

4.17

1.76

9.8

3.7

23.4

24.2

mmol/l

—

(3007853) Bacteria identified in Skin by Aerobe culture

2.69

1.74

1.9

1.6

—

(3002582) Erythrocytes [#/volume] in Urine

112

2.19

1.70

7.4

3.3

11.2

618.1

e6/l

0.51

(3007164) IgA [Mass/volume] in Serum or Plasma

2.32

1.66

5.6

1.4

1.7

2.7

g/l

—

(46237023) Hepatitis B virus core and surface Ab and surface Ag panel - Serum

3.87

1.66

1.4

1.2

—

(3029879) Epithelial cells.squamous [#/volume] in Urine by Automated count

2.40

1.61

4.3

3.0

1.7

2.3

e6/l

—

(3018010) Neutrophils/100 leukocytes in Blood

167

2.09

1.61

27.4

5.1

59.2

57.6

0.30

157

(3015736) pH of Urine

140

2.10

1.61

6.0

3.5

—

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

3.13

1.56

2.7

1.5

—

(40761535) Cells panel - Urine sediment

2.98

1.49

4.5

3.5

—

(3044640) Blood type and Crossmatch panel - Blood

118

2.04

1.45

3.3

2.1

—

(3042936) Bacteria identified in Isolate by Culture

2.31

1.41

3.5

3.1

—

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

2.05

1.36

3.3

2.1

—

(3018095) Leukocytes [#/volume] in Urine

129

1.97

1.36

9.0

4.1

14.2

63.3

e6/l

1.59

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

318

0.53

1.22

4.6

4.1

1.3

1.2

mmol/l

0.19

295

(3000494) Fungus identified in Specimen by Culture

2.15

1.15

1.5

2.0

—

(3023368) Bacteria identified in Blood by Culture

101

1.90

1.13

7.8

4.9

—

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

145

1.82

1.13

9.0

2.6

70.7

91.6

ug/l

0.51

134

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

1.96

1.09

2.1

1.7

1.8

0.9

mg/l

—

(3036481) Cortisol [Moles/volume] in Serum or Plasma

2.18

1.05

1.4

1.9

257.3

368.3

nmol/l

—

(3002109) Cholesterol in LDL/Cholesterol in HDL [Mass Ratio] in Serum or Plasma

0.00

1.00

0.0

1.6

—

(3019832) Treponema pallidum Ab [Presence] in Serum

0.00

0.99

0.0

1.6

—

(3037467) Urinalysis macro (dipstick) panel - Urine

247

1.78

0.98

8.4

4.3

—

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

1.94

0.82

1.5

1.3

—

(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

2.31

0.79

2.2

1.4

—

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

2.31

0.79

1.4

—

(3000991) Gas panel - Venous blood

2.12

0.75

26.4

14.2

—

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

1.83

0.74

1.3

—

(3019060) Gas panel - Arterial blood

2.03

0.73

3.0

22.6

—

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

105

1.64

0.72

2.7

2.2

161.1

186.0

u/l

0.17

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

1.69

0.68

2.4

1.7

—

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

1.75

0.68

2.2

1.7

—

(3009343) pH of Capillary blood

0.00

0.62

0.0

1.3

—

(43534045) MCM6 gene c.-13910C>T and -13915T>G [Identifier] in Blood or Tissue by Molecular genetics method Nominal

0.00

0.61

0.0

1.0

—

(21494755) Public health laboratory ask at order entry panel

0.00

0.61

0.0

1.1

—

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

1.76

0.59

14.3

7.3

—

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

101

1.56

0.58

1.9

3.1

53.1

54.6

u/l

0.07

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

1.65

0.52

2.4

1.6

—

(40760892) CBC W Ordered Manual Differential panel - Blood

1.56

0.51

12.5

4.2

—

(3002256) Pathology report gross observation

1.61

0.51

1.0

1.3

—

(3022217) INR in Platelet poor plasma by Coagulation assay

1.58

0.50

30.7

26.0

—

1.5

—

(3022145) Colonoscopy Study observation

1.58

0.50

1.9

1.4

—

(3033319) Streptococcus pyogenes Ag [Presence] in Throat

1.58

0.43

1.4

—

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

1.58

0.43

4.2

1.5

—

(3022313) Gas panel - Capillary blood

0.00

0.42

0.0

1.3

—

(3044491) Cholesterol non HDL [Mass/volume] in Serum or Plasma

0.00

0.42

0.0

1.5

—

(40768793) Breast Pathology biopsy report

0.00

0.42

0.0

1.3

—

(3021584) Pregnancy associated plasma protein A [Units/volume] in Serum or Plasma

0.00

0.41

0.0

1.5

—

(36660697) Celiac disease serology panel - Serum

1.48

0.40

1.2

1.1

—

(3019800) Troponin T.cardiac [Mass/volume] in Serum or Plasma

137

1.38

0.40

3.8

58.0

71.8

ng/l

0.11

(3003785) Carcinoembryonic Ag [Mass/volume] in Serum or Plasma

1.42

0.36

5.7

5.5

4.6

107.0

ug/l

—

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

1.38

0.35

2.0

1.5

—

(3041096) Erythrocytes [Presence] in Urine by Automated

0.69

0.35

9.1

3.3

—

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

322

1.36

0.31

32.2

14.4

81.0

79.2

ml/min/173m2

0.18

256

(3026493) Urate [Moles/volume] in Serum or Plasma

1.33

0.25

3.5

2.4

316.4

8234.9

umol/l

0.79

(3026008) Bacteria identified in Urine by Culture

128

1.26

0.22

5.2

2.6

—

(4034850)

0.00

0.21

0.0

13.5

—

(3043238) Trisomy 21 risk [Likelihood] in Fetus

0.00

0.21

0.0

1.5

—

(40763531) Fetal Nuchal fold [Multiple of the median] Thickness adjusted for maternal weight

0.00

0.21

0.0

1.2

—

(46235831) Pregnancy associated plasma protein A [Multiple of the median] adjusted in Serum or Plasma

0.00

0.21

0.0

1.2

—

(3049207) Fetal Trisomy 21 risk [Likelihood] Based on maternal age

0.00

0.21

0.0

1.2

—

(3005033) Fetal Nuchal fold Thickness US

0.00

0.21

0.0

1.2

—

(42529200) Cancer Ag 15-3 [Units/volume] in Serum or Plasma by Immunoassay

0.00

0.21

0.0

3.0

—

104.4

—

(3047352) Trisomy 18 risk [Likelihood] in Fetus

0.00

0.21

0.0

1.2

—

(3008714) Choriogonadotropin [Multiple of the median] adjusted in Serum or Plasma

0.00

0.21

0.0

1.2

—

(3019145) Choriogonadotropin.beta subunit free [Mass/volume] in Serum or Plasma

0.00

0.21

0.0

1.6

—

(3050129) First trimester maternal screen panel - Serum or Plasma

0.00

0.21

0.0

1.2

—

(3010156) C reactive protein [Mass/volume] in Serum or Plasma by High sensitivity method

0.00

0.21

0.0

1.8

—

2.2

—

(3004490) Bicarbonate [Moles/volume] standard in Capillary blood

0.00

0.20

0.0

1.4

—

23.9

—

(3044889) 12 lead EKG panel

241

0.83

0.18

4.8

3.7

—

(3009035) Cobalamin (Vitamin B12) [Moles/volume] in Serum or Plasma

1.19

0.18

1.8

358.6

492.0

pmol/l

—

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

0.72

0.17

3.8

5.1

2.7

2.1

ug/l

—

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

184

1.15

0.12

4.7

4.2

—

(40768804) Tissue Pathology biopsy report

155

1.15

0.11

2.8

2.2

—

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

126

1.16

0.10

7.3

3.7

—

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

1.15

0.09

1.2

1.8

—

(3013512) EKG study

0.89

0.07

4.6

4.0

—

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

201

0.91

0.06

3.7

3.2

—

(3009542) Hematocrit [Volume Fraction] of Blood

300

1.10

0.05

45.7

17.8

39.7

40.3

0.32

219

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

103

0.96

0.00

1.2

1.4

—

(40761511) CBC panel - Blood by Automated count

353

0.96

0.00

23.4

14.1

—

(3002385) Erythrocyte distribution width [Ratio]

286

1.04

0.00

45.3

19.2

14.3

13.8

1.07

280

(3000924) Streptococcus pyogenes [Presence] in Throat by Organism specific culture

0.00

0.0

1.5

—

(3032155) Metanephrine Free [Moles/volume] in Serum or Plasma

0.00

0.0

1.2

—

(3030408) 3-Methoxytyramine [Moles/volume] in Serum or Plasma

0.00

0.0

1.2

—

(3011288) Drugs identified in Urine by Screen method

0.00

0.0

1.1

—

(3009340) Metanephrine [Moles/volume] in Serum or Plasma

0.00

0.0

1.2

—

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

0.00

0.0

1.7

—

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

0.00

0.0

1.8

—

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

0.00

0.0

1.6

—

(3027475) Erythrocytes [#/volume] in Cerebral spinal fluid

0.00

0.0

1.2

—

314.2

—

(3016543) Leukocytes [#/volume] in Cerebral spinal fluid

0.00

0.0

1.0

—

3.7

—

(3019050) Tissue transglutaminase IgA Ab [Units/volume] in Serum

0.92

0.00

1.4

1.1

—

1.8

—

(1617658) Protocol used for examination of sentinel lymph nodes

0.00

0.0

1.0

—

(40760888) Immunoglobulin light chains.free panel - Serum

0.00

0.0

3.6

—

(40764126) Parainfluenza virus RNA [Presence] in Specimen by NAA with probe detection

0.00

0.0

2.0

—

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

0.00

0.0

1.2

—

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

0.00

0.0

1.6

—

(3027315) Oxygen [Partial pressure] in Blood

0.00

0.0

3.9

—

7.9

—

(44816752) ERBB2 gene copy number/nucleus in Tissue by FISH

0.00

0.0

1.2

—

(4024509)

0.00

0.0

1.2

—

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

0.00

0.0

1.2

—

(3005570) Glucose [Moles/volume] in Urine

0.00

0.0

2.7

—

(3030136) 5-Hydroxyindoleacetate [Moles/volume] in Serum or Plasma

0.00

0.0

1.5

—

50.0

—

(3029511) Human papilloma virus DNA [Presence] in Specimen by NAA with probe detection

0.00

0.0

1.2

—

(3013290) Carbon dioxide [Partial pressure] in Blood

0.00

0.0

3.9

—

5.2

—

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

0.00

0.0

3.2

—

1.7

—

(3008898) HLA-B27 [Presence]

0.00

0.0

1.0

—

(3010421) pH of Blood

0.00

0.0

4.0

—

7.4

—

(3028369) Herpes simplex virus 1+2 DNA [Presence] in Specimen by NAA with probe detection

0.00

0.0

1.6

—

(3010566) Parathyrin.intact [Moles/volume] in Serum or Plasma

0.00

0.0

2.1

—

(3020321) Streptococcus agalactiae [Presence] in Vaginal fluid by Organism specific culture

0.00

0.0

1.4

—

(3019473) Protein [Mass/volume] in Cerebral spinal fluid

0.00

0.0

1.2

—

306.2

—

(3022806) Fractional oxyhemoglobin in Capillary blood

0.00

0.0

3.6

—

88.9

—

(3014702) Chromogranin A [Moles/volume] in Serum or Plasma

0.00

0.0

2.6

—

2.6

—

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

0.00

0.0

1.7

—

Mortality – FinRegistry

↥

Association

Association between endpoint D3_CVID_TCELL and mortality.

Females

No data

Males

No data

Mortality risk

Mortality risk for people of age

years, who have D3_CVID_TCELL.

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_CVID_TCELL – Common variable immunodeficiency with predominant abnormalities of T-cell numbers and function

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

Common variable immunodeficiency with predominant abnormalities of T-cell numbers and function

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