SHROOM4
Basic information
Region (hg38): X:50586796-50814302
Links
Phenotypes
GenCC
Source:
- X-linked intellectual disability, Stocco dos Santos type (Supportive), mode of inheritance: XL
- X-linked intellectual disability, Stocco dos Santos type (Limited), mode of inheritance: XL
- X-linked complex neurodevelopmental disorder (Disputed Evidence), mode of inheritance: XL
- complex neurodevelopmental disorder (Limited), mode of inheritance: XL
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Intellectual developmental disorder, X-linked, Stocco dos Santos type | XL | General | Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Musculoskeletal; Neurologic | 2063914; 12673656; 16249884 |
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (187 variants)
- not_provided (89 variants)
- X-linked_intellectual_disability,_Stocco_dos_Santos_type (37 variants)
- SHROOM4-related_disorder (30 variants)
- History_of_neurodevelopmental_disorder (4 variants)
- Intellectual_disability (3 variants)
- See_cases (2 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SHROOM4 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000020717.5. Only rare variants are included in the table.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
---|---|---|---|---|---|---|
synonymous | 19 | 27 | ||||
missense | 205 | 34 | 15 | 254 | ||
nonsense | 4 | |||||
start loss | 0 | |||||
frameshift | 1 | |||||
splice donor/acceptor (+/-2bp) | 2 | |||||
Total | 0 | 1 | 213 | 55 | 19 |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
SHROOM4 | protein_coding | protein_coding | ENST00000376020 | 9 | 222656 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
1.00 | 0.000349 | 125492 | 24 | 230 | 125746 | 0.00101 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.951 | 502 | 566 | 0.887 | 0.0000428 | 9762 |
Missense in Polyphen | 122 | 173.55 | 0.70297 | 2953 | ||
Synonymous | 0.330 | 212 | 218 | 0.972 | 0.0000160 | 2958 |
Loss of Function | 5.31 | 4 | 40.5 | 0.0988 | 0.00000304 | 690 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00112 | 0.00106 |
Ashkenazi Jewish | 0.0161 | 0.00987 |
East Asian | 0.00 | 0.00 |
Finnish | 0.000497 | 0.000323 |
European (Non-Finnish) | 0.00160 | 0.000897 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.000656 | 0.000327 |
Other | 0.00257 | 0.00163 |
dbNSFP
Source:
- Function
- FUNCTION: Probable regulator of cytoskeletal architecture that plays an important role in development. May regulate cellular and cytoskeletal architecture by modulating the spatial distribution of myosin II (By similarity). {ECO:0000250, ECO:0000269|PubMed:16684770}.;
- Disease
- DISEASE: Note=A chromosomal aberration involving SHROOM4 is a cause of X-linked mental retardation (XLMR). Translocation t(X;8)(p11.22;p23.3) with FBXO25.; DISEASE: Note=A chromosomal aberration involving SHROOM4 is a cause of X-linked mental retardation (XLMR). Translocation t(X;19).;
Recessive Scores
- pRec
- 0.0827
Intolerance Scores
- loftool
- 0.179
- rvis_EVS
- 1.07
- rvis_percentile_EVS
- 91.71
Haploinsufficiency Scores
- pHI
- 0.142
- hipred
- N
- hipred_score
- 0.426
- ghis
- 0.489
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.0584
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Shroom4
- Phenotype
- immune system phenotype; vision/eye phenotype; hematopoietic system phenotype;
Gene ontology
- Biological process
- cell morphogenesis;actin filament organization;brain development;actin cytoskeleton organization;cognition
- Cellular component
- stress fiber;cytoplasm;actin filament;adherens junction;cytoplasmic side of plasma membrane;basal plasma membrane;actin cytoskeleton;apical plasma membrane;cortical actin cytoskeleton;apical junction complex
- Molecular function
- myosin II binding;actin filament binding