SRCAP
Basic information
Region (hg38): 16:30698209-30741409
Links
Phenotypes
GenCC
Source:
- Floating-Harbor syndrome (Definitive), mode of inheritance: AD
- Floating-Harbor syndrome (Supportive), mode of inheritance: AD
- Floating-Harbor syndrome (Definitive), mode of inheritance: AD
- developmental delay, hypotonia, musculoskeletal defects, and behavioral abnormalities (Definitive), mode of inheritance: AD
- developmental delay, hypotonia, musculoskeletal defects, and behavioral abnormalities (Strong), mode of inheritance: AD
- Floating-Harbor syndrome (Strong), mode of inheritance: AD
- Floating-Harbor syndrome (Definitive), mode of inheritance: AD
- developmental delay, hypotonia, musculoskeletal defects, and behavioral abnormalities (Strong), mode of inheritance: AD
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Floating-Harbor syndrome; Developmental delay, hypotonia, musculoskeletal defects, and behavioral abnormalities | AD | 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 | Craniofacial; Genitourinary; Musculoskeletal; Neurologic | 7588969; 16523514; 20358590; 22265015; 23763483; 33909990 |
ClinVar
This is a list of variants' phenotypes submitted to
- not_provided (1600 variants)
- Floating-Harbor_syndrome (502 variants)
- Developmental_delay,_hypotonia,_musculoskeletal_defects,_and_behavioral_abnormalities (468 variants)
- Inborn_genetic_diseases (390 variants)
- not_specified (108 variants)
- SRCAP-related_disorder (85 variants)
- Neurodevelopmental_disorder (31 variants)
- Intellectual_disability (5 variants)
- See_cases (5 variants)
- Autism_spectrum_disorder (2 variants)
- Microcephaly (2 variants)
- Intellectual_disability,_moderate (1 variants)
- Congenital_heart_disease (1 variants)
- Epilepsy (1 variants)
- Cleft_lip/palate (1 variants)
- 46,XY_disorder_of_sex_development (1 variants)
- Neurodevelopmental_delay (1 variants)
- Developmental_delay (1 variants)
- Rare_genetic_intellectual_disability (1 variants)
- Non-syndromic_intellectual_disability (1 variants)
- Multiple_congenital_anomalies/dysmorphic_syndrome (1 variants)
- Developmental_disorder (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SRCAP gene is commonly pathogenic or not. These statistics are base on transcript: NM_000006662.3. 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 | 17 | 458 | 11 | 486 | ||
missense | 1127 | 175 | 1313 | |||
nonsense | 15 | 18 | 39 | |||
start loss | 0 | |||||
frameshift | 26 | 35 | 68 | |||
splice donor/acceptor (+/-2bp) | 11 | |||||
Total | 42 | 66 | 1161 | 633 | 15 |
Highest pathogenic variant AF is 0.000185915
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
SRCAP | protein_coding | protein_coding | ENST00000262518 | 32 | 46073 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
1.00 | 2.73e-16 | 125732 | 0 | 16 | 125748 | 0.0000636 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 2.13 | 1634 | 1.89e+3 | 0.862 | 0.000118 | 20343 |
Missense in Polyphen | 147 | 225.75 | 0.65117 | 2176 | ||
Synonymous | -3.11 | 850 | 742 | 1.15 | 0.0000419 | 7482 |
Loss of Function | 9.81 | 6 | 124 | 0.0485 | 0.00000754 | 1310 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000185 | 0.000185 |
Ashkenazi Jewish | 0.000199 | 0.000198 |
East Asian | 0.00 | 0.00 |
Finnish | 0.0000464 | 0.0000462 |
European (Non-Finnish) | 0.0000709 | 0.0000615 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.0000981 | 0.0000980 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Catalytic component of the SRCAP complex which mediates the ATP-dependent exchange of histone H2AZ/H2B dimers for nucleosomal H2A/H2B, leading to transcriptional regulation of selected genes by chromatin remodeling. Acts as a coactivator for CREB-mediated transcription, steroid receptor-mediated transcription, and Notch-mediated transcription. {ECO:0000269|PubMed:10347196, ECO:0000269|PubMed:11522779, ECO:0000269|PubMed:14500758, ECO:0000269|PubMed:16024792, ECO:0000269|PubMed:16634648, ECO:0000269|PubMed:17617668}.;
- Disease
- DISEASE: Floating-Harbor syndrome (FLHS) [MIM:136140]: A rare genetic disorder characterized by proportionate short stature, delayed bone age, delayed speech development, and typical facial features. The face is triangular with deep-set eyes, long eyelashes, bulbous nose, wide columella, short philtrum, and thin lips. {ECO:0000269|PubMed:22265015}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
- Pathway
- Pathways Affected in Adenoid Cystic Carcinoma
(Consensus)
Recessive Scores
- pRec
- 0.0771
Intolerance Scores
- loftool
- 0.00579
- rvis_EVS
- -4.14
- rvis_percentile_EVS
- 0.15
Haploinsufficiency Scores
- pHI
- 0.405
- hipred
- Y
- hipred_score
- 0.630
- ghis
- 0.626
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.847
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Srcap
- Phenotype
Gene ontology
- Biological process
- chromatin remodeling;regulation of transcription by RNA polymerase II;viral process;gene silencing;histone acetylation;ATP-dependent chromatin remodeling;histone exchange;positive regulation of nucleic acid-templated transcription
- Cellular component
- Swr1 complex;nucleus;nucleoplasm;Golgi apparatus;nuclear body;protein-containing complex;perinuclear region of cytoplasm
- Molecular function
- DNA binding;transcription coactivator activity;helicase activity;histone acetyltransferase activity;protein binding;ATP binding;ATPase activity;histone binding