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 rule None	520210
2. Check conditions None	520210
3. Check pre-conditions, main-only, mode, registry filters Registry filters: Hospital discharge: ICD-10 — D84.0 Cause of death: ICD-10 — D84.0 2 out of 7 registries used, show all original rules.	34
4. Check minimum number of events None	34
5. Include endpoints None	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

NAME	D3_LYMPHOANTIGEN1DEF
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	D840
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	D840
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 Lymphocyte function antigen-1 [LFA-1] defect 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	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

↥

(ID) Name

N Cases

N Controls

-log₁₀(p)

cases

controls

cases

controls

unit

-log₁₀(p)

N cases

N controls

(3000494) Fungus identified in Specimen by Culture

6.03

3.53

2.3

1.7

—

(40758558) Short blood count panel - Blood

3.08

2.42

7.3

6.5

—

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

0.00

2.10

0.0

1.4

—

(4010399)

4.31

1.78

1.2

1.5

—

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

2.67

1.38

1.4

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

3.07

1.33

2.2

1.3

—

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

3.07

1.33

2.6

1.3

—

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

2.51

1.32

1.9

3.2

20.0

19.9

—

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

2.37

1.25

1.7

3.1

11.1

12.2

umol/l

—

(3023368) Bacteria identified in Blood by Culture

2.19

1.25

4.5

4.1

—

(3007853) Bacteria identified in Skin by Aerobe culture

2.67

1.21

6.4

1.7

—

(42870588) Differential panel, method unspecified - Blood

2.15

1.20

9.7

5.9

—

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

2.18

1.12

3.3

1.6

—

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

2.25

1.07

2.4

1.7

—

(3037522) Nuclear Ab [Titer] in Serum

2.48

1.07

1.4

1.5

—

365.7

—

(3048816) Calcium.ionized [Moles/volume] adjusted to pH 7.4 in Blood

0.00

1.03

0.0

5.4

—

1.2

—

(3022096) Basophils/100 leukocytes in Blood

101

1.87

0.91

12.1

7.1

0.6

0.08

(3006504) Eosinophils/100 leukocytes in Blood

103

1.82

0.84

12.1

7.2

2.4

2.5

0.04

(3002173) Hemoglobin [Mass/volume] in Arterial blood

0.00

0.81

0.0

7.3

—

122.0

—

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

1.81

0.81

4.1

3.5

—

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

2.06

0.80

1.9

3.0

2.4

2.2

g/l

—

(3019069) Monocytes/100 leukocytes in Blood

105

1.77

0.78

12.2

7.3

9.9

8.8

0.54

(36304419) Bacteria [Presence] in Urine

1.84

0.77

3.5

3.2

—

(3003458) Phosphate [Moles/volume] in Serum or Plasma

1.89

0.75

5.9

1.0

1.1

mmol/l

—

(3044889) 12 lead EKG panel

155

1.71

0.71

4.0

4.3

—

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

1.92

0.69

18.2

12.7

—

(3029187) Natriuretic peptide.B prohormone N-Terminal [Mass/volume] in Serum or Plasma

100

1.68

0.66

4.1

3.5

3142.0

2572.9

ng/l

0.16

(3018010) Neutrophils/100 leukocytes in Blood

110

1.65

0.64

12.0

6.9

63.6

60.4

0.36

100

(3028653) Carboxyhemoglobin/Hemoglobin.total in Arterial blood

0.00

0.62

0.0

7.1

—

1.6

—

(3006217) Methemoglobin/Hemoglobin.total in Arterial blood

0.00

0.62

0.0

8.4

—

0.7

—

(3008152) Bicarbonate [Moles/volume] in Arterial blood

0.00

0.62

0.0

5.1

—

24.3

—

(3014007) Fractional oxyhemoglobin in Arterial blood

0.00

0.62

0.0

8.8

—

92.3

—

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

106

0.57

0.62

3.4

3.7

—

(3002030) Lymphocytes/100 leukocytes in Blood

111

1.63

0.61

12.2

7.1

22.7

25.3

0.40

102

(3042936) Bacteria identified in Isolate by Culture

1.70

0.58

5.3

1.9

—

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

104

1.59

0.55

5.4

4.9

48.8

37.8

ng/l

—

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

1.64

0.51

3.9

5.1

—

(3026008) Bacteria identified in Urine by Culture

1.53

0.46

3.2

3.5

—

(40768797) Stomach Pathology biopsy report

1.78

0.46

1.6

1.1

—

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

1.51

0.44

4.4

2.5

76.6

75.3

nmol/l

0.06

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

187

1.50

0.44

14.0

6.5

86.8

80.2

u/l

0.26

176

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

1.49

0.43

2.7

2.4

3.2

3.3

mg/l

—

(3018418) pH of Serum or Plasma

1.53

0.43

8.3

5.7

—

7.4

—

(40768804) Tissue Pathology biopsy report

1.53

0.43

1.9

2.1

—

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

0.00

0.42

0.0

2.9

—

1.6

—

(3031040) Bacteria [#/volume] in Urine by Automated count

168

1.46

0.41

5.7

5.8

—

9794.8

—

(3009508) Creatinine [Moles/volume] in Urine

1.50

0.37

3.4

3.0

7.3

mmol/l

—

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

1.50

0.37

2.1

2.0

93.2

50.5

u/l

—

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

107

0.67

0.36

3.7

5.7

—

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

0.70

0.27

3.0

5.7

1.0

2.4

ug/l

—

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

0.00

0.22

0.0

10.6

—

(4034850)

0.00

0.22

0.0

18.5

—

(3019832) Treponema pallidum Ab [Presence] in Serum

0.00

0.21

0.0

1.7

—

(3033319) Streptococcus pyogenes Ag [Presence] in Throat

0.00

0.20

0.0

1.1

—

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

1.29

0.19

3.3

3.1

118.1

104.4

ug/l

0.09

(3009542) Hematocrit [Volume Fraction] of Blood

173

1.22

0.15

31.4

20.2

36.7

36.5

0.02

103

(3015736) pH of Urine

109

1.16

0.07

3.4

4.9

—

(3037467) Urinalysis macro (dipstick) panel - Urine

170

1.13

0.05

5.8

5.4

—

(40761511) CBC panel - Blood by Automated count

226

1.05

0.00

27.6

15.3

—

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

115

1.07

0.00

3.5

2.8

—

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

232

0.97

0.00

18.7

10.7

21.9

22.9

u/l

0.13

221

(3020564) Creatinine [Moles/volume] in Serum or Plasma

228

1.03

0.00

35.2

21.2

86.7

87.5

umol/l

0.03

228

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

201

0.99

0.00

28.0

18.3

72.4

71.3

ml/min/173m2

0.06

157

(4094501)

0.00

0.0

1.4

—

(3012441) Differential panel - Pleural fluid

0.00

0.0

1.0

—

(1761868) Lipid panel - Serum or Plasma

0.86

0.00

2.2

3.2

—

(3044640) Blood type and Crossmatch panel - Blood

0.95

0.00

2.6

2.0

—

(3043405) Microscopic observation [Identifier] in Specimen by Non-gynecological cytology method

0.00

0.0

1.8

—

(3019150) Specific gravity of Urine by Refractometry

0.96

0.00

4.0

6.2

—

1.0

—

(3045414) Leukocytes [Presence] in Urine

0.00

0.0

1.3

—

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

0.00

0.0

1.7

—

(36032269) Testosterone Free [Moles/volume] in Serum or Plasma by calculation

0.00

0.0

1.9

—

210.4

—

(3043238) Trisomy 21 risk [Likelihood] in Fetus

0.00

0.0

1.7

—

(40768800) Prostate Pathology biopsy report

0.00

0.0

1.2

—

(3004248) Sex hormone binding globulin [Moles/volume] in Serum or Plasma

0.00

0.0

2.3

—

40.3

—

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

0.00

0.0

1.2

—

(3045424) Erythrocytes [Presence] in Urine

0.00

0.0

1.0

—

(40768795) Lymph node Pathology biopsy report

0.00

0.0

1.2

—

(3005570) Glucose [Moles/volume] in Urine

0.00

0.0

1.2

—

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

0.00

0.0

1.2

—

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

0.00

0.0

1.1

—

1.3

—

(3022806) Fractional oxyhemoglobin in Capillary blood

0.00

0.0

1.0

—

89.5

—

(3022914) Cancer Ag 19-9 [Units/volume] in Serum or Plasma

0.00

0.0

3.2

—

34.9

—

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

0.00

0.0

1.3

—

(3030366) Cystatin C [Mass/volume] in Serum or Plasma

0.00

0.0

3.1

—

2.4

—

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

0.00

0.0

1.8

—

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

0.00

0.0

1.8

—

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

0.00

0.0

1.3

—

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

0.00

0.0

1.9

—

(3013512) EKG study

0.93

0.00

3.7

4.6

—

(3047352) Trisomy 18 risk [Likelihood] in Fetus

0.00

0.0

1.8

—

(3033705) Calcium.ionized [Moles/volume] in Venous blood

0.00

0.0

1.8

—

(3023150) Myeloperoxidase Ab [Units/volume] in Serum

0.00

0.0

1.2

—

(40760847) Basement membrane Ab [Titer] in Serum by Immunofluorescence

0.00

0.0

1.2

—

(3035285) Chloride [Moles/volume] in Venous blood

0.00

0.0

1.8

—

109.6

—

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

0.00

0.0

1.8

—

(3005033) Fetal Nuchal fold Thickness US

0.00

0.0

1.8

—

(3017569) Oxygen content in Arterial blood

0.00

0.0

2.0

—

(37019628) Gastrointestinal bacterial pathogens panel - Stool by NAA with probe detection

0.00

0.0

1.2

—

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

0.00

0.0

1.0

—

(42868544) Hantavirus puumala IgM Ab [Presence] in Serum or Plasma by Immunofluorescence

0.00

0.0

1.0

—

(40768806) Pleura Pathology biopsy report

0.00

0.0

1.3

—

(3025839) Triglyceride [Moles/volume] in Serum or Plasma

1.02

0.00

1.3

1.5

1.3

mmol/l

—

(3041354) Potassium [Moles/volume] in Venous blood

0.00

0.0

1.8

—

3.9

—

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

0.00

0.0

1.8

—

(3037756) Immunofixation for Serum or Plasma

0.00

0.0

1.3

—

(3042111) Morphology [Interpretation] in Bone marrow Narrative

0.00

0.0

1.2

—

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

0.00

0.0

1.7

—

(40763082) Lactate dehydrogenase [Enzymatic activity/volume] in Pleural fluid by Lactate to pyruvate reaction

0.00

0.0

1.3

—

145.8

—

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

0.00

0.0

1.5

—

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]

rg [CI]

Hits

Coloc Hits

FinRegistry

FinnGen

FinRegistry

FinnGen

Loading data

Lymphocyte function antigen-1 [LFA-1] defect

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