chr16:31265490:G>A Detail (hg38) (ITGAM, LOC126862331)

Information

Genome

Assembly Position
hg19 chr16:31,276,811-31,276,811 View the variant detail on this assembly version.
hg38 chr16:31,265,490-31,265,490

HGVS

Type Transcript Protein
RefSeq NM_001145808.1:c.230G>A NP_001139280.1:p.Arg77His
Ensemble ENST00000544665.9:c.230G>A ENST00000544665.9:p.Arg77His
ENST00000648685.1:c.230G>A ENST00000648685.1:p.Arg77His
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:<0.001
ToMMo:<0.001
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.008

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 120980 OMIM
HGNC 6149 HGNC
Ensembl ENSG00000169896 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv55278711 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2024-01-31 criteria provided, single submitter not provided germline Detail
Benign 2019-11-12 criteria provided, single submitter ITGAM-related disorder germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.012 Lupus Erythematosus, Systemic Secondly, using a comprehensive imputation-based association test, we found that... BeFree 19129174 Detail
0.003 Kidney Diseases ITGAM coding variant (rs1143679) influences the risk of renal disease, discoid r... BeFree 19939855 Detail
0.002 Lupus Erythematosus, Discoid The rs1143679 (R77H) lupus associated variant of ITGAM (CD11b) impairs complemen... BeFree 22586164 Detail
0.002 lupus erythematosus The rs1143679 (R77H) lupus associated variant of ITGAM (CD11b) impairs complemen... BeFree 22586164 Detail
0.279 Lupus Erythematosus, Systemic [The genetic contribution towards predicting early-onset disease in patients wit... GAD 20881011 Detail
0.279 Lupus Erythematosus, Systemic ITGAM Arg77His is associated with disease susceptibility, arthritis, and renal s... BeFree 20666624 Detail
0.279 Lupus Erythematosus, Systemic The variant of CD11b, rs1143679 within ITGAM, is associated with systemic lupus ... BeFree 24269694 Detail
0.002 lupus erythematosus Combined protein- and nucleic acid-level effects of rs1143679 (R77H), a lupus-pr... BeFree 24608226 Detail
0.279 Lupus Erythematosus, Systemic ITGAM coding variant (rs1143679) influences the risk of renal disease, discoid r... BeFree 19939855 Detail
0.279 Lupus Erythematosus, Systemic A systemic lupus erythematosus-associated R77H substitution in the CD11b chain o... BeFree 21454473 Detail
0.002 Lupus Erythematosus, Discoid Combined protein- and nucleic acid-level effects of rs1143679 (R77H), a lupus-pr... BeFree 24608226 Detail
0.279 Lupus Erythematosus, Systemic The rs1143679 (R77H) lupus associated variant of ITGAM (CD11b) impairs complemen... BeFree 22586164 Detail
0.004 arthritis ITGAM Arg77His is associated with disease susceptibility, arthritis, and renal s... BeFree 20666624 Detail
0.279 Lupus Erythematosus, Systemic The A-allele of ICAM1-ICAM4-ICAM5 rs3093030, associated with elevated plasma lev... BeFree 22523428 Detail
0.002 Lupus Vulgaris Combined protein- and nucleic acid-level effects of rs1143679 (R77H), a lupus-pr... BeFree 24608226 Detail
0.002 Lupus Vulgaris The rs1143679 (R77H) lupus associated variant of ITGAM (CD11b) impairs complemen... BeFree 22586164 Detail
<0.001 Autoimmune Diseases Evaluation of genetic association between an ITGAM non-synonymous SNP (rs1143679... BeFree 21840425 Detail
0.279 Lupus Erythematosus, Systemic Combined protein- and nucleic acid-level effects of rs1143679 (R77H), a lupus-pr... BeFree 24608226 Detail
0.121 rheumatoid arthritis A characteristic single-nucleotide polymorphism (SNP) in each of 9 genetic facto... BeFree 19714582 Detail
0.125 rheumatoid arthritis A characteristic single-nucleotide polymorphism (SNP) in each of 9 genetic facto... BeFree 19714582 Detail
<0.001 rheumatoid arthritis A characteristic single-nucleotide polymorphism (SNP) in each of 9 genetic facto... BeFree 19714582 Detail
0.003 rheumatoid arthritis A characteristic single-nucleotide polymorphism (SNP) in each of 9 genetic facto... BeFree 19714582 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000632.4(ITGAM):c.230G>A (p.Arg77His) AND not provided ClinVar Detail
NM_000632.4(ITGAM):c.230G>A (p.Arg77His) AND ITGAM-related disorder ClinVar Detail
Secondly, using a comprehensive imputation-based association test, we found that ITGAM is one of the... DisGeNET Detail
ITGAM coding variant (rs1143679) influences the risk of renal disease, discoid rash and immunologica... DisGeNET Detail
The rs1143679 (R77H) lupus associated variant of ITGAM (CD11b) impairs complement receptor 3 mediate... DisGeNET Detail
The rs1143679 (R77H) lupus associated variant of ITGAM (CD11b) impairs complement receptor 3 mediate... DisGeNET Detail
[The genetic contribution towards predicting early-onset disease in patients with SLE is quantified ... DisGeNET Detail
ITGAM Arg77His is associated with disease susceptibility, arthritis, and renal symptoms in systemic ... DisGeNET Detail
The variant of CD11b, rs1143679 within ITGAM, is associated with systemic lupus erythematosus and cl... DisGeNET Detail
Combined protein- and nucleic acid-level effects of rs1143679 (R77H), a lupus-predisposing variant w... DisGeNET Detail
ITGAM coding variant (rs1143679) influences the risk of renal disease, discoid rash and immunologica... DisGeNET Detail
A systemic lupus erythematosus-associated R77H substitution in the CD11b chain of the Mac-1 integrin... DisGeNET Detail
Combined protein- and nucleic acid-level effects of rs1143679 (R77H), a lupus-predisposing variant w... DisGeNET Detail
The rs1143679 (R77H) lupus associated variant of ITGAM (CD11b) impairs complement receptor 3 mediate... DisGeNET Detail
ITGAM Arg77His is associated with disease susceptibility, arthritis, and renal symptoms in systemic ... DisGeNET Detail
The A-allele of ICAM1-ICAM4-ICAM5 rs3093030, associated with elevated plasma levels of soluble ICAM1... DisGeNET Detail
Combined protein- and nucleic acid-level effects of rs1143679 (R77H), a lupus-predisposing variant w... DisGeNET Detail
The rs1143679 (R77H) lupus associated variant of ITGAM (CD11b) impairs complement receptor 3 mediate... DisGeNET Detail
Evaluation of genetic association between an ITGAM non-synonymous SNP (rs1143679) and multiple autoi... DisGeNET Detail
Combined protein- and nucleic acid-level effects of rs1143679 (R77H), a lupus-predisposing variant w... DisGeNET Detail
A characteristic single-nucleotide polymorphism (SNP) in each of 9 genetic factors, ITGAM (rs1143679... DisGeNET Detail
A characteristic single-nucleotide polymorphism (SNP) in each of 9 genetic factors, ITGAM (rs1143679... DisGeNET Detail
A characteristic single-nucleotide polymorphism (SNP) in each of 9 genetic factors, ITGAM (rs1143679... DisGeNET Detail
A characteristic single-nucleotide polymorphism (SNP) in each of 9 genetic factors, ITGAM (rs1143679... DisGeNET Detail

Overlapped Transcript Coordinates

Gene Transcript ID Exon Number Chromosome Start Stop Type Amino Mutation Transcript Position Links

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs1143679 dbSNP
Genome
hg38
Position
chr16:31,265,490-31,265,490
Variant Type
snv
Reference Allele
G
Alternative Allele
A
Filtering Status (HGVD)
PASS
Filtering Status (HGVD)
LowQual
# of samples (HGVD)
1191
Mean of sample read depth (HGVD)
39.57
Standard deviation of sample read depth (HGVD)
17.48
Number of reference allele (HGVD)
2381
Number of alternative allele (HGVD)
1
Allele Frequency (HGVD)
4.1981528127623844E-4
Gene Symbol (HGVD)
ITGAM
ToMMo VCF FILTER column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
PASS
Total VCF ID column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
rs1143679
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0001
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
1
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
3856
East Asian Allele Counts (ExAC)
29
East Asian Heterozygous Counts (ExAC)
29
East Asian Homozygous Counts (ExAC)
0
East Asian Allele Frequency (ExAC)
0.007520746887966805
Chromosome Counts in All Race (ExAC)
61830
Allele Counts in All Race (ExAC)
8997
Heterozygous Counts in All Race (ExAC)
8021
Homozygous Counts in All Race (ExAC)
488
Allele Frequency in All Race (ExAC)
0.1455118874332848
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