LAMA1Laminin, alpha 1
Autism Reports / Total Reports
6 / 12Rare Variants / Common Variants
18 / 1Aliases
LAMA1, LAMA, S-LAM-alphaAssociated Syndromes
Tourette syndrome, Poretti-Boltshauser syndromeChromosome Band
18p11.31Associated Disorders
-Relevance to Autism
A SNP within the LAMA1 gene showed association in the secondary analyses in a combined AGP GWA sample (Anney et al., 2012).
Molecular Function
Binding to cells via a high affinity receptor, laminin is thought to mediate the attachment, migration and organization of cells into tissues during embryonic development by interacting with other extracellular matrix components.
External Links
SFARI Genomic Platforms
Reports related to LAMA1 (12 Reports)
| # | Type | Title | Author, Year | Autism Report | Associated Disorders |
|---|---|---|---|---|---|
| 1 | Primary | Individual common variants exert weak effects on the risk for autism spectrum disorders | Anney R , et al. (2012) | Yes | - |
| 2 | Support | Synaptic, transcriptional and chromatin genes disrupted in autism | De Rubeis S , et al. (2014) | Yes | - |
| 3 | Support | The contribution of de novo coding mutations to autism spectrum disorder | Iossifov I et al. (2014) | Yes | - |
| 4 | Support | Large-scale discovery of novel genetic causes of developmental disorders | Deciphering Developmental Disorders Study (2014) | No | - |
| 5 | Positive Association | De Novo Coding Variants Are Strongly Associated with Tourette Disorder | Willsey AJ , et al. (2017) | No | - |
| 6 | Support | Exome sequencing of 457 autism families recruited online provides evidence for autism risk genes | Feliciano P et al. (2019) | Yes | - |
| 7 | Support | De Novo Damaging DNA Coding Mutations Are Associated With Obsessive-Compulsive Disorder and Overlap With Tourette's Disorder and Autism | Cappi C , et al. (2019) | No | - |
| 8 | Support | - | Mitani T et al. (2021) | No | - |
| 9 | Support | - | Brea-Fernández AJ et al. (2022) | No | - |
| 10 | Support | - | Zhou X et al. (2022) | Yes | - |
| 11 | Support | - | Cirnigliaro M et al. (2023) | Yes | - |
| 12 | Support | - | et al. () | No | - |
Rare Variants (18)
| Status | Allele Change | Residue Change | Variant Type | Inheritance Pattern | Parental Transmission | Family Type | PubMed ID | Author, Year |
|---|---|---|---|---|---|---|---|---|
| c.3512C>T | p.Thr1171Met | missense_variant | De novo | - | - | 35982159 | Zhou X et al. (2022) | |
| c.5297C>T | p.Ala1766Val | missense_variant | De novo | - | - | 35982159 | Zhou X et al. (2022) | |
| c.7260G>A | p.Pro2420%3D | synonymous_variant | De novo | - | - | 35982159 | Zhou X et al. (2022) | |
| c.1434G>A | p.Glu478= | synonymous_variant | De novo | - | - | 31452935 | Feliciano P et al. (2019) | |
| c.7460G>T | p.Arg2487Leu | missense_variant | De novo | - | Simplex | 35982159 | Zhou X et al. (2022) | |
| c.8215G>C | p.Val2739Leu | missense_variant | De novo | - | Simplex | 31771860 | Cappi C , et al. (2019) | |
| c.7917G>A | p.Met2639Ile | missense_variant | De novo | - | Simplex | 25363768 | Iossifov I et al. (2014) | |
| c.8215G>C | p.Val2739Leu | missense_variant | De novo | - | Simplex | 28472652 | Willsey AJ , et al. (2017) | |
| c.2236G>A | p.Gly746Ser | missense_variant | De novo | - | Simplex | 25363760 | De Rubeis S , et al. (2014) | |
| c.1034del | p.Gln345ArgfsTer5 | frameshift_variant | Familial | Maternal | Simplex | 38041506 | et al. () | |
| c.858+1G>T | - | splice_site_variant | Familial | Maternal | Multiplex | 37506195 | Cirnigliaro M et al. (2023) | |
| c.1504G>T | p.Glu502Ter | stop_gained | Familial | Both parents | Multiplex | 34582790 | Mitani T et al. (2021) | |
| c.2035A>T | p.Lys679Ter | stop_gained | Familial | Maternal | Multiplex | 37506195 | Cirnigliaro M et al. (2023) | |
| c.3038_3039del | p.Glu1013ValfsTer13 | frameshift_variant | Familial | Paternal | Simplex | 38041506 | et al. () | |
| c.1862C>T | p.Thr621Ile | missense_variant | Familial | Paternal | - | 35322241 | Brea-Fernández AJ et al. (2022) | |
| c.2527G>A | p.Gly843Ser | missense_variant | Familial | Maternal | - | 35322241 | Brea-Fernández AJ et al. (2022) | |
| c.3428_3429insACCCCCTGGGCTGCAGCCC | p.Asn1143LysfsTer50 | frameshift_variant | De novo | - | - | 35982159 | Zhou X et al. (2022) | |
| c.8214G>T | p.Ser2738= | synonymous_variant | De novo | - | Unknown | 25533962 | Deciphering Developmental Disorders Study (2014) |
Common Variants (1)
| Status | Allele Change | Residue Change | Variant Type | Inheritance Pattern | Paternal Transmission | Family Type | PubMed ID | Author, Year |
|---|---|---|---|---|---|---|---|---|
| c.1840-257C>T | - | intron_variant | - | - | - | 22843504 | Anney R , et al. (2012) |
SFARI Gene score
2
Strong Candidate
A SNP within the LAMA1 gene showed association in the secondary analyses in a combined AGP GWA sample with a P-value of 3.578E07 (PMID 22843504).
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
A SNP within the LAMA1 gene showed association in the secondary analyses in a combined AGP GWA sample with a P-value of 3.578E07 (PMID 22843504).
1/1/2020
3
3
Decreased from 3 to 3
Description
A SNP within the LAMA1 gene showed association in the secondary analyses in a combined AGP GWA sample with a P-value of 3.578E07 (PMID 22843504).
10/1/2019
4
3
Decreased from 4 to 3
New Scoring Scheme
Description
A SNP within the LAMA1 gene showed association in the secondary analyses in a combined AGP GWA sample with a P-value of 3.578E07 (PMID 22843504).
4/1/2017
4
4
Decreased from 4 to 4
Description
A SNP within the LAMA1 gene showed association in the secondary analyses in a combined AGP GWA sample with a P-value of 3.578E?07 (PMID 22843504).
Reports Added
[Individual common variants exert weak effects on the risk for autism spectrum disorderspi.2012] [Large-scale discovery of novel genetic causes of developmental disorders.2014] [Synaptic, transcriptional and chromatin genes disrupted in autism.2014] [The contribution of de novo coding mutations to autism spectrum disorder2014] [De Novo Coding Variants Are Strongly Associated with Tourette Disorder.2017]1/1/2016
4
4
Decreased from 4 to 4
Description
A SNP within the LAMA1 gene showed association in the secondary analyses in a combined AGP GWA sample with a P-value of 3.578E?07 (PMID 22843504).
Reports Added
[Individual common variants exert weak effects on the risk for autism spectrum disorderspi.2012] [Large-scale discovery of novel genetic causes of developmental disorders.2014] [Synaptic, transcriptional and chromatin genes disrupted in autism.2014] [The contribution of de novo coding mutations to autism spectrum disorder2014]7/1/2015
4
Increased from to 4
Description
A SNP within the LAMA1 gene showed association in the secondary analyses in a combined AGP GWA sample with a P-value of 3.578E?07 (PMID 22843504).
Krishnan Probability Score
Score 0.4944647221175
Ranking 3639/25841 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 1.3917613183766E-24
Ranking 18084/18225 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 0.94685065241181
Ranking 17037/18665 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).
Larsen Cumulative Evidence Score
Score 3
Ranking 349/461 scored genes
[Show Scoring Methodology]
Larsen and colleagues generated gene scores based on the sum of evidence for all available
ASD-associated variants in a gene, with assessments based on mode of inheritance, effect size,
and variant frequency in the general population. The approach was first presented in Mol Autism
7:44 (2016), and scores for 461 genes can be found in column I in supplementary table 4 from
that paper.
Zhang D Score
Score -0.21265472114023
Ranking 15695/20870 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.