Human Gene Module / Chromosome 12 / KRR1

KRR1KRR1, small subunit (SSU) processome component, homolog (yeast)

SFARI Gene Score
2
Strong Candidate Criteria 2.1
Autism Reports / Total Reports
3 / 3
Rare Variants / Common Variants
3 / 2
Aliases
KRR1, HRB2,  RIP-1
Associated Syndromes
-
Chromosome Band
12q21.2
Associated Disorders
-
Relevance to Autism

Two SNPs within 100 kb of the KRR1 gene (one intronic, one 500B downstream of the gene) showed association with ASD in a case-control analysis in the Taiwanese Han population (Kuo et al., 2015).

Molecular Function

The protein encoded by the KRR1 gene is required for 40S ribosome biogenesis and is involved in nucleolar processing of pre-18S ribosomal RNA and ribosome assembly.

SFARI Genomic Platforms
Reports related to KRR1 (3 Reports)
# Type Title Author, Year Autism Report Associated Disorders
1 Primary Genome-Wide Association Study for Autism Spectrum Disorder in Taiwanese Han Population Kuo PH , et al. (2015) Yes -
2 Support Inherited and De Novo Genetic Risk for Autism Impacts Shared Networks Ruzzo EK , et al. (2019) Yes -
3 Support - Cirnigliaro M et al. (2023) Yes -
Rare Variants   (3)
Status Allele Change Residue Change Variant Type Inheritance Pattern Parental Transmission Family Type PubMed ID Author, Year
c.661-2_661-1insTTTA - splice_site_variant Familial Maternal Multiplex 37506195 Cirnigliaro M et al. (2023)
c.567_568del p.Val190PhefsTer7 frameshift_variant Familial Maternal Multiplex 31398340 Ruzzo EK , et al. (2019)
c.939_940insGAGA p.Gln314GlufsTer13 frameshift_variant De novo - Multiplex 37506195 Cirnigliaro M et al. (2023)
Common Variants   (2)
Status Allele Change Residue Change Variant Type Inheritance Pattern Paternal Transmission Family Type PubMed ID Author, Year
c.1004-383A>G - intron_variant - - - 26398136 Kuo PH , et al. (2015)
c.*2336A>G - 500B_downstream_variant - - - 26398136 Kuo PH , et al. (2015)
SFARI Gene score
2

Strong Candidate

Two SNPs within 100 kb of the KRR1 gene (one intronic, one 500B downstream of the gene) showed association with ASD in a case-control analysis in the Taiwanese Han population (Kuo et al., 2015).

Score Delta: Score remained at 2

2

Strong Candidate

See all Category 2 Genes

We 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
icon
2

Decreased from 3 to 2

Description

Two SNPs within 100 kb of the KRR1 gene (one intronic, one 500B downstream of the gene) showed association with ASD in a case-control analysis in the Taiwanese Han population (Kuo et al., 2015).

10/1/2019
4
icon
3

Decreased from 4 to 3

New Scoring Scheme
Description

Two SNPs within 100 kb of the KRR1 gene (one intronic, one 500B downstream of the gene) showed association with ASD in a case-control analysis in the Taiwanese Han population (Kuo et al., 2015).

Reports Added
[New Scoring Scheme]
7/1/2019
4
icon
4

Decreased from 4 to 4

Description

Two SNPs within 100 kb of the KRR1 gene (one intronic, one 500B downstream of the gene) showed association with ASD in a case-control analysis in the Taiwanese Han population (Kuo et al., 2015).

10/1/2015
icon
4

Increased from to 4

Description

Two SNPs within 100 kb of the KRR1 gene (one intronic, one 500B downstream of the gene) showed association with ASD in a case-control analysis in the Taiwanese Han population (Kuo et al., 2015).

Krishnan Probability Score

Score 0.49301633971064

Ranking 4319/25841 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 0.019350580570581

Ranking 9442/18225 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 0.81642131247998

Ranking 2527/18665 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 0.46561355194256

Ranking 784/20870 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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