This is a non-core endpoint: only basic statistics are computed.
See these related core endpoints for full statistics:
Lymphocyte function antigen-1 [LFA-1] defect
D3_LYMPHOANTIGEN1DEF
No definition available.
Endpoint definition
↥
Endpoint definition steps |
FinnGen |
|---|---|
Phenotype data |
520210 |
1. Apply sex-specific ruleNone |
520210 |
2. Check conditionsNone |
520210 |
3. Check pre-conditions, main-only, mode, registry filtersRegistry filters: 2 out of 7 registries used, show all original rules. |
34 |
4. Check minimum number of eventsNone |
34 |
5. Include endpointsNone |
34 |
6. Filter based on genotype QC (FinnGen only) |
34 |
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
- D84
- Name in latin
- Deficientia antigeni 1 functionis lymphocytorum
Similar endpoints
↥List of similar endpoints to
Lymphocyte function antigen-1 [LFA-1] defect
based on the number of shared cases.
Similar with more cases:
- Other immunodeficiencies
- Immunodeficiencies
- Certain disorders involving the immune mechanism
- Diseases of the blood and blood-forming organs and certain disorders involving the immune mechanism
- Any operation in hilmo
Similar with less cases:
None
Case counts by codes
↥
Summary Statistics
↥-FinRegistry-
Key figures
| All | Female | Male | |
|---|---|---|---|
| Number of individuals | |||
| Whole population | 457 | 301 | 152 |
| Only index persons | 324 | 210 | 114 |
| Unadjusted period prevalence (%) | |||
| Whole population | 0.01 | 0.01 | 0.00 |
| Only index persons | 0.01 | 0.01 | 0.00 |
| Median age at first event (years) | |||
| Whole population | 72.31 | 73.57 | 69.59 |
| Only index persons | 70.92 | 72.46 | 68.07 |
-FinnGen-
Key figures
| All | Female | Male | |
|---|---|---|---|
| Number of individuals | 34 | 15 | 19 |
| Unadjusted period prevalence (%) | 0.01 | 0.01 | 0.01 |
| Median age at first event (years) | 67.64 | 63.55 | 70.86 |
-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
↥OMOP Concept
People with measurements
Mean N measurements
Mean measured value
(ID) Name
N Cases
N Controls
OR
-log10(p)
cases
controls
unit
cases
controls
-log10(p)
N cases
N controls
(3000494) Fungus identified in Specimen by Culture
9
19
6.03
3.53
2.3
1.7
—
—
—
0
0
(40758558) Short blood count panel - Blood
14
63
3.08
2.42
7.3
6.5
—
—
—
0
0
(3003694) ABO and Rh group [Type] in Blood
0
53
0.00
2.10
0.0
1.4
—
—
—
0
0
(4010399)
5
13
4.31
1.78
1.2
1.5
—
—
—
0
0
(3043924) Respiratory syncytial virus RNA [Identifier] in Specimen by NAA with probe detection
8
35
2.67
1.38
1.4
1.5
—
—
—
0
0
(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
5
18
3.07
1.33
2.2
1.3
—
—
—
0
0
(3051552) Clostridioides difficile toxin genes [Presence] in Stool by NAA with probe detection
5
18
3.07
1.33
2.6
1.3
—
—
—
0
0
(40763571) Iron/Transferrin [Ratio] in Serum or Plasma
8
37
2.51
1.32
1.9
3.2
%
20.0
19.9
—
8
31
(3022948) Iron [Moles/volume] in Serum or Plasma
8
39
2.37
1.25
1.7
3.1
umol/l
11.1
12.2
—
8
34
(3023368) Bacteria identified in Blood by Culture
13
75
2.19
1.25
4.5
4.1
—
—
—
0
0
(3007853) Bacteria identified in Skin by Aerobe culture
7
30
2.67
1.21
6.4
1.7
—
—
—
0
0
(42870588) Differential panel, method unspecified - Blood
13
76
2.15
1.20
9.7
5.9
—
—
—
0
0
(3044938) Influenza virus A RNA [Presence] in Specimen by NAA with probe detection
9
48
2.18
1.12
3.3
1.6
—
—
—
0
0
(3038288) Influenza virus B RNA [Presence] in Specimen by NAA with probe detection
7
35
2.25
1.07
2.4
1.7
—
—
—
0
0
(3037522) Nuclear Ab [Titer] in Serum
5
22
2.48
1.07
1.4
1.5
—
365.7
—
0
7
(3048816) Calcium.ionized [Moles/volume] adjusted to pH 7.4 in Blood
0
30
0.00
1.03
0.0
5.4
—
1.2
—
0
21
(3022096) Basophils/100 leukocytes in Blood
15
101
1.87
0.91
12.1
7.1
%
0.6
0.6
0.08
15
92
(3006504) Eosinophils/100 leukocytes in Blood
15
103
1.82
0.84
12.1
7.2
%
2.4
2.5
0.04
15
95
(3002173) Hemoglobin [Mass/volume] in Arterial blood
0
27
0.00
0.81
0.0
7.3
—
122.0
—
0
27
(3029287) Urinalysis microscopic panel [#/volume] - Urine by Automated count
14
95
1.81
0.81
4.1
3.5
—
—
—
0
0
(3004789) Transferrin [Mass/volume] in Serum or Plasma
7
38
2.06
0.80
1.9
3.0
g/l
2.4
2.2
—
7
33
(3019069) Monocytes/100 leukocytes in Blood
15
105
1.77
0.78
12.2
7.3
%
9.9
8.8
0.54
15
97
(36304419) Bacteria [Presence] in Urine
11
70
1.84
0.77
3.5
3.2
—
—
—
0
0
(3003458) Phosphate [Moles/volume] in Serum or Plasma
7
41
1.89
0.75
5.9
5.9
mmol/l
1.0
1.1
—
7
34
(3044889) 12 lead EKG panel
20
155
1.71
0.71
4.0
4.3
—
—
—
0
0
(3045783) Sodium and Potassium panel [Moles/volume] - Serum or Plasma
5
28
1.92
0.69
18.2
12.7
—
—
—
0
0
(3029187) Natriuretic peptide.B prohormone N-Terminal [Mass/volume] in Serum or Plasma
14
100
1.68
0.66
4.1
3.5
ng/l
3142.0
2572.9
0.16
14
85
(3018010) Neutrophils/100 leukocytes in Blood
15
110
1.65
0.64
12.0
6.9
%
63.6
60.4
0.36
15
100
(3028653) Carboxyhemoglobin/Hemoglobin.total in Arterial blood
0
20
0.00
0.62
0.0
7.1
—
1.6
—
0
20
(3006217) Methemoglobin/Hemoglobin.total in Arterial blood
0
20
0.00
0.62
0.0
8.4
—
0.7
—
0
20
(3008152) Bicarbonate [Moles/volume] in Arterial blood
0
20
0.00
0.62
0.0
5.1
—
24.3
—
0
20
(3014007) Fractional oxyhemoglobin in Arterial blood
0
19
0.00
0.62
0.0
8.8
—
92.3
—
0
19
(3001079) Blood group antibody screen [Presence] in Serum or Plasma
7
106
0.57
0.62
3.4
3.7
—
—
—
0
0
(3002030) Lymphocytes/100 leukocytes in Blood
15
111
1.63
0.61
12.2
7.1
%
22.7
25.3
0.40
15
102
(3042936) Bacteria identified in Isolate by Culture
6
38
1.70
0.58
5.3
1.9
—
—
—
0
0
(3019800) Troponin T.cardiac [Mass/volume] in Serum or Plasma
14
104
1.59
0.55
5.4
4.9
ng/l
48.8
37.8
—
7
79
(3011397) Hemoglobin [Presence] in Urine by Test strip
10
69
1.64
0.51
3.9
5.1
—
—
—
0
0
(3026008) Bacteria identified in Urine by Culture
13
98
1.53
0.46
3.2
3.5
—
—
—
0
0
(40768797) Stomach Pathology biopsy report
5
30
1.78
0.46
1.6
1.1
—
—
—
0
0
(40771025) 25-Hydroxyvitamin D3+25-Hydroxyvitamin D2 [Moles/volume] in Serum or Plasma
13
99
1.51
0.44
4.4
2.5
nmol/l
76.6
75.3
0.06
13
81
(3035995) Alkaline phosphatase [Enzymatic activity/volume] in Serum or Plasma
22
187
1.50
0.44
14.0
6.5
u/l
86.8
80.2
0.26
22
176
(3015399) Transferrin receptor.soluble [Mass/volume] in Serum or Plasma
9
66
1.49
0.43
2.7
2.4
mg/l
3.2
3.3
—
9
56
(3018418) pH of Serum or Plasma
11
81
1.53
0.43
8.3
5.7
—
7.4
—
0
18
(40768804) Tissue Pathology biopsy report
11
81
1.53
0.43
1.9
2.1
—
—
—
0
0
(3018405) Lactate [Moles/volume] in Arterial blood
0
15
0.00
0.42
0.0
2.9
—
1.6
—
0
15
(3031040) Bacteria [#/volume] in Urine by Automated count
20
168
1.46
0.41
5.7
5.8
—
9794.8
—
0
6
(3009508) Creatinine [Moles/volume] in Urine
10
74
1.50
0.37
3.4
3.0
mmol/l
7.3
7.3
—
10
64
(3016771) Amylase [Enzymatic activity/volume] in Serum or Plasma
10
74
1.50
0.37
2.1
2.0
u/l
93.2
50.5
—
10
67
(40763086) Leukocyte esterase [Presence] in Urine by Automated test strip
8
107
0.67
0.36
3.7
5.7
—
—
—
0
0
(3013603) Prostate specific Ag [Mass/volume] in Serum or Plasma
7
92
0.70
0.27
3.0
5.7
ug/l
1.0
2.4
—
7
78
(40762366) Oxygen capacity [Volume Fraction] in Arterial blood
0
11
0.00
0.22
0.0
10.6
—
—
—
0
0
(4034850)
0
10
0.00
0.22
0.0
18.5
—
—
—
0
0
(3019832) Treponema pallidum Ab [Presence] in Serum
0
13
0.00
0.21
0.0
1.7
—
—
—
0
0
(3033319) Streptococcus pyogenes Ag [Presence] in Throat
0
14
0.00
0.20
0.0
1.1
—
—
—
0
0
(3001122) Ferritin [Mass/volume] in Serum or Plasma
11
92
1.29
0.19
3.3
3.1
ug/l
118.1
104.4
0.09
11
85
(3009542) Hematocrit [Volume Fraction] of Blood
19
173
1.22
0.15
31.4
20.2
%
36.7
36.5
0.02
12
103
(3015736) pH of Urine
12
109
1.16
0.07
3.4
4.9
—
—
—
0
0
(3037467) Urinalysis macro (dipstick) panel - Urine
18
170
1.13
0.05
5.8
5.4
—
—
—
0
0
(40761511) CBC panel - Blood by Automated count
23
226
1.05
0.00
27.6
15.3
—
—
—
0
0
(706163) SARS-CoV-2 (COVID-19) RNA [Presence] in Respiratory system specimen by NAA with probe detection
12
115
1.07
0.00
3.5
2.8
—
—
—
0
0
(3006923) Alanine aminotransferase [Enzymatic activity/volume] in Serum or Plasma
23
232
0.97
0.00
18.7
10.7
u/l
21.9
22.9
0.13
23
221
(3020564) Creatinine [Moles/volume] in Serum or Plasma
23
228
1.03
0.00
35.2
21.2
umol/l
86.7
87.5
0.03
23
228
(40764999) Glomerular filtration rate/1.73 sq M.predicted [Volume Rate/Area] in Serum, Plasma or Blood by Creatinine-based formula (CKD-EPI)
20
201
0.99
0.00
28.0
18.3
ml/min/173m2
72.4
71.3
0.06
20
157
(4094501)
0
5
0.00
0.00
0.0
1.4
—
—
—
0
0
(3012441) Differential panel - Pleural fluid
0
5
0.00
0.00
0.0
1.0
—
—
—
0
0
(1761868) Lipid panel - Serum or Plasma
5
57
0.86
0.00
2.2
3.2
—
—
—
0
0
(3044640) Blood type and Crossmatch panel - Blood
7
73
0.95
0.00
2.6
2.0
—
—
—
0
0
(3043405) Microscopic observation [Identifier] in Specimen by Non-gynecological cytology method
0
5
0.00
0.00
0.0
1.8
—
—
—
0
0
(3019150) Specific gravity of Urine by Refractometry
6
62
0.96
0.00
4.0
6.2
—
1.0
—
0
9
(3045414) Leukocytes [Presence] in Urine
0
7
0.00
0.00
0.0
1.3
—
—
—
0
0
(3019145) Choriogonadotropin.beta subunit free [Mass/volume] in Serum or Plasma
0
7
0.00
0.00
0.0
1.7
—
—
—
0
0
(36032269) Testosterone Free [Moles/volume] in Serum or Plasma by calculation
0
7
0.00
0.00
0.0
1.9
—
210.4
—
0
7
(3043238) Trisomy 21 risk [Likelihood] in Fetus
0
7
0.00
0.00
0.0
1.7
—
—
—
0
0
(40768800) Prostate Pathology biopsy report
0
5
0.00
0.00
0.0
1.2
—
—
—
0
0
(3004248) Sex hormone binding globulin [Moles/volume] in Serum or Plasma
0
7
0.00
0.00
0.0
2.3
—
40.3
—
0
7
(3000855) Microscopic observation [Identifier] in Vaginal fluid by Gram stain
0
5
0.00
0.00
0.0
1.2
—
—
—
0
0
(3045424) Erythrocytes [Presence] in Urine
0
5
0.00
0.00
0.0
1.0
—
—
—
0
0
(40768795) Lymph node Pathology biopsy report
0
5
0.00
0.00
0.0
1.2
—
—
—
0
0
(3005570) Glucose [Moles/volume] in Urine
0
5
0.00
0.00
0.0
1.2
—
—
—
0
0
(3020321) Streptococcus agalactiae [Presence] in Vaginal fluid by Organism specific culture
0
5
0.00
0.00
0.0
1.2
—
—
—
0
0
(3028271) Lactate [Moles/volume] in Capillary blood
0
7
0.00
0.00
0.0
1.1
—
1.3
—
0
7
(3022806) Fractional oxyhemoglobin in Capillary blood
0
6
0.00
0.00
0.0
1.0
—
89.5
—
0
6
(3022914) Cancer Ag 19-9 [Units/volume] in Serum or Plasma
0
9
0.00
0.00
0.0
3.2
—
34.9
—
0
9
(3006093) Chlamydia trachomatis DNA [Presence] in Specimen by NAA with probe detection
0
8
0.00
0.00
0.0
1.3
—
—
—
0
0
(3030366) Cystatin C [Mass/volume] in Serum or Plasma
0
8
0.00
0.00
0.0
3.1
—
2.4
—
0
8
(3008714) Choriogonadotropin [Multiple of the median] adjusted in Serum or Plasma
0
6
0.00
0.00
0.0
1.8
—
—
—
0
0
(3049207) Fetal Trisomy 21 risk [Likelihood] Based on maternal age
0
6
0.00
0.00
0.0
1.8
—
—
—
0
0
(3002109) Cholesterol in LDL/Cholesterol in HDL [Mass Ratio] in Serum or Plasma
0
9
0.00
0.00
0.0
1.3
—
—
—
0
0
(36032419) SARS-CoV-2 (COVID-19) Ag [Presence] in Upper respiratory specimen by Immunoassay
0
9
0.00
0.00
0.0
1.9
—
—
—
0
0
(3013512) EKG study
7
74
0.93
0.00
3.7
4.6
—
—
—
0
0
(3047352) Trisomy 18 risk [Likelihood] in Fetus
0
6
0.00
0.00
0.0
1.8
—
—
—
0
0
(3033705) Calcium.ionized [Moles/volume] in Venous blood
0
8
0.00
0.00
0.0
1.8
—
—
—
0
0
(3023150) Myeloperoxidase Ab [Units/volume] in Serum
0
6
0.00
0.00
0.0
1.2
—
—
—
0
0
(40760847) Basement membrane Ab [Titer] in Serum by Immunofluorescence
0
6
0.00
0.00
0.0
1.2
—
—
—
0
0
(3035285) Chloride [Moles/volume] in Venous blood
0
8
0.00
0.00
0.0
1.8
—
109.6
—
0
8
(46235831) Pregnancy associated plasma protein A [Multiple of the median] adjusted in Serum or Plasma
0
6
0.00
0.00
0.0
1.8
—
—
—
0
0
(3005033) Fetal Nuchal fold Thickness US
0
6
0.00
0.00
0.0
1.8
—
—
—
0
0
(3017569) Oxygen content in Arterial blood
0
6
0.00
0.00
0.0
2.0
—
—
—
0
0
(37019628) Gastrointestinal bacterial pathogens panel - Stool by NAA with probe detection
0
6
0.00
0.00
0.0
1.2
—
—
—
0
0
(43534045) MCM6 gene c.-13910C>T and -13915T>G [Identifier] in Blood or Tissue by Molecular genetics method Nominal
0
8
0.00
0.00
0.0
1.0
—
—
—
0
0
(42868544) Hantavirus puumala IgM Ab [Presence] in Serum or Plasma by Immunofluorescence
0
6
0.00
0.00
0.0
1.0
—
—
—
0
0
(40768806) Pleura Pathology biopsy report
0
6
0.00
0.00
0.0
1.3
—
—
—
0
0
(3025839) Triglyceride [Moles/volume] in Serum or Plasma
6
59
1.02
0.00
1.3
1.5
mmol/l
1.5
1.3
—
6
50
(3041354) Potassium [Moles/volume] in Venous blood
0
8
0.00
0.00
0.0
1.8
—
3.9
—
0
8
(40763531) Fetal Nuchal fold [Multiple of the median] Thickness adjusted for maternal weight
0
6
0.00
0.00
0.0
1.8
—
—
—
0
0
(3037756) Immunofixation for Serum or Plasma
0
6
0.00
0.00
0.0
1.3
—
—
—
0
0
(3042111) Morphology [Interpretation] in Bone marrow Narrative
0
6
0.00
0.00
0.0
1.2
—
—
—
0
0
(3021584) Pregnancy associated plasma protein A [Units/volume] in Serum or Plasma
0
9
0.00
0.00
0.0
1.7
—
—
—
0
0
(40763082) Lactate dehydrogenase [Enzymatic activity/volume] in Pleural fluid by Lactate to pyruvate reaction
0
6
0.00
0.00
0.0
1.3
—
145.8
—
0
6
(3050129) First trimester maternal screen panel - Serum or Plasma
0
6
0.00
0.00
0.0
1.5
—
—
—
0
0
Mortality – FinRegistry
↥Association
Association between endpoint D3_LYMPHOANTIGEN1DEF and mortality.
Females
| Parameter | HR [95% CI] | p-value |
|---|---|---|
| D3_LYMPHOANTIGEN1DEF | 1.865 [1.44, 2.41] | < 0.001 |
| Birth year | 0.993 [0.98, 1.0] | 0.118 |
During the follow-up period (1.1.1998 — 31.12.2019), 162 out of 259 females with D3_LYMPHOANTIGEN1DEF died.
Males
| Parameter | HR [95% CI] | p-value |
|---|---|---|
| D3_LYMPHOANTIGEN1DEF | 1.915 [1.3, 2.81] | < 0.001 |
| Birth year | 0.986 [0.98, 1.0] | 0.005 |
During the follow-up period (1.1.1998 — 31.12.2019), 79 out of 132 males with D3_LYMPHOANTIGEN1DEF died.
Mortality risk
Mortality risk for people of age
years, who have D3_LYMPHOANTIGEN1DEF.| N-year risk | Females | Males |
|---|---|---|
| 1 | 0.226% | 0.398% |
| 5 | 1.029% | 2.144% |
| 10 | 2.443% | 5.328% |
| 15 | 4.653% | 9.974% |
| 20 | 8.153% | 16.766% |
Relationships between endpoints
↥Index endpoint: D3_LYMPHOANTIGEN1DEF – Lymphocyte function antigen-1 [LFA-1] defect
GWS hits: -
Endpoint
Case Overlap
Survival Analysis
Genetic Correlations
Genetic Signals
N (Jaccard index)
HR [CI]
Extremity
rg [CI]
Extremity
Hits
Coloc Hits
FinRegistry
FinnGen
FinRegistry
FinnGen
FinnGen
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