HLA-BMajor histocompatibility complex, class I, B
Autism Reports / Total Reports
5 / 5Rare Variants / Common Variants
0 / 3Aliases
HLA-B, AS, HLAB, SPDA1Associated Syndromes
-Chromosome Band
6p21.33Associated Disorders
-Relevance to Autism
Different alleles of the HLA-B gene have been shown to nominally associate with ASD in case-control studies using two different populations (Al-Hakbany et al., 2014; Puangpetch et al., 2015).
Molecular Function
HLA-B belongs to the HLA class I heavy chain paralogues; class I molecules play a central role in the immune system by presenting peptides derived from the endoplasmic reticulum lumen.
External Links
SFARI Genomic Platforms
Reports related to HLA-B (5 Reports)
| # | Type | Title | Author, Year | Autism Report | Associated Disorders |
|---|---|---|---|---|---|
| 1 | Primary | The Relationship of HLA Class I and II Alleles and Haplotypes with Autism: A Case Control Study | Al-Hakbany M , et al. (2014) | Yes | - |
| 2 | Negative Association | DNA typing of HLA-A, -C, -B, AND -DRB1 in the children with autism in the Republic of Macedonia | Trajkovski V and Spiroski M (2015) | Yes | - |
| 3 | Positive Association | Significant Association of HLA-B Alleles and Genotypes in Thai Children with Autism Spectrum Disorders: A Case-Control Study | Puangpetch A , et al. (2016) | Yes | - |
| 4 | Negative Association | Association of HLA alleles with autism | Sayad A , et al. (2018) | Yes | - |
| 5 | Positive Association | Immunity and mental illness: findings from a Danish population-based immunogenetic study of seven psychiatric and neurodevelopmental disorders | Nudel R , et al. (2019) | Yes | - |
Rare Variants
No rare variants reported.
Common Variants (3)
| Status | Allele Change | Residue Change | Variant Type | Inheritance Pattern | Paternal Transmission | Family Type | PubMed ID | Author, Year |
|---|---|---|---|---|---|---|---|---|
| - | - | allele | - | - | - | 30976114 | Nudel R , et al. (2019) | |
| - | - | allele | - | - | - | 24672722 | Al-Hakbany M , et al. (2014) | |
| - | - | allele | - | - | - | 26819491 | Puangpetch A , et al. (2016) |
SFARI Gene score
2
Strong Candidate
Different alleles of the HLA-B gene have been shown to nominally associate with ASD in case-control studies using two different populations (Al-Hakbany et al., 2014; Puangpetch et al., 2015).
Score Delta: Score remained at 2
criteria met
See SFARI Gene'scoring criteriaWe considered a rigorous statistical comparison between cases and controls, yielding genome-wide statistical significance, with independent replication, to be the strongest possible evidence for a gene. These criteria were relaxed slightly for category 2.
4/1/2022
3
2
Decreased from 3 to 2
Description
Different alleles of the HLA-B gene have been shown to nominally associate with ASD in case-control studies using two different populations (Al-Hakbany et al., 2014; Puangpetch et al., 2015).
10/1/2019
4
3
Decreased from 4 to 3
New Scoring Scheme
Description
Different alleles of the HLA-B gene have been shown to nominally associate with ASD in case-control studies using two different populations (Al-Hakbany et al., 2014; Puangpetch et al., 2015).
Reports Added
[New Scoring Scheme]4/1/2019
4
4
Decreased from 4 to 4
Description
Different alleles of the HLA-B gene have been shown to nominally associate with ASD in case-control studies using two different populations (Al-Hakbany et al., 2014; Puangpetch et al., 2015).
1/1/2019
4
4
Decreased from 4 to 4
Description
Different alleles of the HLA-B gene have been shown to nominally associate with ASD in case-control studies using two different populations (Al-Hakbany et al., 2014; Puangpetch et al., 2015).
Reports Added
[Association of HLA alleles with autism.2018]1/1/2016
4
Increased from to 4
Description
Different alleles of the HLA-B gene have been shown to nominally associate with ASD in case-control studies using two different populations (Al-Hakbany et al., 2014; Puangpetch et al., 2015).
Krishnan Probability Score
Score 0.52058169352658
Ranking 1695/25841 scored genes
[Show Scoring Methodology]
Krishnan and colleagues generated probability scores genome-wide by using a machine learning
approach on a human brain-specific gene network. The method was first presented in Nat
Neurosci 19, 1454-1462 (2016), and scores for more than 25,000 RefSeq genes can be accessed
in column G of supplementary table 3 (see:
http://www.nature.com/neuro/journal/v19/n11/extref/nn.4353-S5.xlsx). A searchable browser,
with the ability to view networks of associated ASD risk genes, can be found at
asd.princeton.edu.
ExAC Score
Score 0.002664634636856
Ranking 11078/18225 scored genes
[Show Scoring Methodology]
The Exome Aggregation Consortium (ExAC) is a summary database of 60,706 exomes that has
been widely used to estimate 'constraint' on mutation for individual genes. It was introduced by
Lek et al. Nature 536, 285-291 (2016), and the ExAC browser can be found at
exac.broadinstitute.org. The pLI score was developed as measure of intolerance to loss-of-
function mutation. A pLI > 0.9 is generally viewed as highly constrained, and thus any loss-of-
function mutations in autism in such a gene would be more likely to confer risk. For a full list of
pLI scores see:
ftp://ftp.broadinstitute.org/pub/ExAC_release/release0.3.1/functional_gene_constraint/fordist_cle
aned_exac_nonTCGA_z_pli_rec_null_data.txt
Sanders TADA Score
Score 0.93093721048372
Ranking 11563/18665 scored genes
[Show Scoring Methodology]
The TADA score ('Transmission and De novo Association') was introduced by He et al. PLoS Genet 9(8):e1003671 (2013),
and is a statistic that integrates evidence from both de novo and transmitted mutations.
It forms the basis for the claim of 65 individual genes being strongly associated with autism risk at a false discovery rate of 0.1 (Sanders et al. Neuron 87, 1215-1233
(2015)). The calculated TADA score for 18,665 RefSeq genes can be found in column P of Supplementary Table 6 in the Sanders et al. paper
(the column headed 'tadaFdrAscSscExomeSscAgpSmallDel'), which represents a combined analysis of exome data and small de novo deletions (see www.cell.com/cms/attachment/2038545319/2052606711/mmc7.xlsx).
Zhang D Score
Score -0.29277350375115
Ranking 17097/20870 scored genes
[Show Scoring Methodology]
The DAMAGES score (disease-associated mutation analysis using gene expression signatures),
or D score, was developed to combine evidence from de novo loss-of- function mutation with
evidence from cell-type- specific gene expression in the mouse brain (specifically translational
profiles of 24 specific mouse CNS cell types isolated from 6 different brain regions). Genes with
positive D scores are more likely to be associated with autism risk, with higher-confidence genes
having higher D scores. This statistic was first presented by Zhang & Shen (Hum Mutat 38, 204-
215 (2017), and D scores for more than 20,000 RefSeq genes can be found in column M in
supplementary table 2 from that paper.
Zhang D Score
Score -0.48248699254921
Ranking 19104/20870 scored genes
[Show Scoring Methodology]
The DAMAGES score (disease-associated mutation analysis using gene expression signatures),
or D score, was developed to combine evidence from de novo loss-of- function mutation with
evidence from cell-type- specific gene expression in the mouse brain (specifically translational
profiles of 24 specific mouse CNS cell types isolated from 6 different brain regions). Genes with
positive D scores are more likely to be associated with autism risk, with higher-confidence genes
having higher D scores. This statistic was first presented by Zhang & Shen (Hum Mutat 38, 204-
215 (2017), and D scores for more than 20,000 RefSeq genes can be found in column M in
supplementary table 2 from that paper.
Zhang D Score
Score -0.55506270720921
Ranking 19645/20870 scored genes
[Show Scoring Methodology]
The DAMAGES score (disease-associated mutation analysis using gene expression signatures),
or D score, was developed to combine evidence from de novo loss-of- function mutation with
evidence from cell-type- specific gene expression in the mouse brain (specifically translational
profiles of 24 specific mouse CNS cell types isolated from 6 different brain regions). Genes with
positive D scores are more likely to be associated with autism risk, with higher-confidence genes
having higher D scores. This statistic was first presented by Zhang & Shen (Hum Mutat 38, 204-
215 (2017), and D scores for more than 20,000 RefSeq genes can be found in column M in
supplementary table 2 from that paper.
Zhang D Score
Score -0.57073607554306
Ranking 19737/20870 scored genes
[Show Scoring Methodology]
The DAMAGES score (disease-associated mutation analysis using gene expression signatures),
or D score, was developed to combine evidence from de novo loss-of- function mutation with
evidence from cell-type- specific gene expression in the mouse brain (specifically translational
profiles of 24 specific mouse CNS cell types isolated from 6 different brain regions). Genes with
positive D scores are more likely to be associated with autism risk, with higher-confidence genes
having higher D scores. This statistic was first presented by Zhang & Shen (Hum Mutat 38, 204-
215 (2017), and D scores for more than 20,000 RefSeq genes can be found in column M in
supplementary table 2 from that paper.