Human Gene Module / Chromosome 18 / LAMA1

LAMA1Laminin, alpha 1

Score
3
Suggestive Evidence Criteria 3.1
Autism Reports / Total Reports
4 / 7
Rare Variants / Common Variants
6 / 1
Aliases
LAMA1, LAMA,  S-LAM-alpha
Associated Syndromes
Tourette syndrome
Genetic Category
Rare Single Gene Mutation, Genetic Association
Chromosome Band
18p11.31
Associated 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.

Reports related to LAMA1 (7 Reports)
# Type Title Author, Year Autism Report Associated Disorders
1 Primary Individual common variants exert weak effects on the risk for autism spectrum disorderspi. 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 -
Rare Variants   (6)
Status Allele Change Residue Change Variant Type Inheritance Pattern Parental Transmission Family Type PubMed ID Author, Year
c.1434G>A p.Glu478%3D synonymous_variant De novo NA - 31452935 Feliciano P , et al. (2019)
c.8215G>C p.Val2739Leu missense_variant De novo NA Simplex 31771860 Cappi C , et al. (2019)
c.7917G>A p.Met2639Ile missense_variant De novo NA Simplex 25363768 Iossifov I , et al. (2014)
c.8215G>C p.Val2739Leu missense_variant De novo NA Simplex 28472652 Willsey AJ , et al. (2017)
c.2236G>A p.Gly746Ser missense_variant De novo NA Simplex 25363760 De Rubeis S , et al. (2014)
c.8214G>T p.Ser2738%3D synonymous_variant De novo NA 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
3

Suggestive Evidence

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 4

3

Suggestive Evidence

See all Category 3 Genes

The literature is replete with relatively small studies of candidate genes, using either common or rare variant approaches, which do not reach the criteria set out for categories 1 and 2. Genes that had two such lines of supporting evidence were placed in category 3, and those with one line of evidence were placed in category 4. Some additional lines of "accessory evidence" (indicated as "acc" in the score cards) could also boost a gene from category 4 to 3.

1/1/2020
4
icon
4

Score remained at 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 3.578E07 (PMID 22843504).

10/1/2019
4
icon
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).

7/1/2015
icon
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.
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