ANKRD11
Basic information
Region (hg38): 16:89267629-89490561
Links
Phenotypes
GenCC
Source:
- KBG syndrome (Definitive), mode of inheritance: AD
- KBG syndrome (Definitive), mode of inheritance: AD
- KBG syndrome (Definitive), mode of inheritance: AD
- KBG syndrome (Supportive), mode of inheritance: AD
- congenital heart defects, multiple types (Limited), mode of inheritance: AD
- KBG syndrome (Strong), mode of inheritance: AD
- KBG syndrome (Definitive), mode of inheritance: AD
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
KBG syndrome | 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; Dental; Musculoskeletal; Neurologic | 15523620; 15378538; 21782149; 22307766; 25125236 |
ClinVar
This is a list of variants' phenotypes submitted to
- KBG syndrome (1243 variants)
- not provided (885 variants)
- Inborn genetic diseases (538 variants)
- not specified (57 variants)
- ANKRD11-related condition (29 variants)
- Global developmental delay (17 variants)
- Intellectual disability (16 variants)
- See cases (8 variants)
- Neurodevelopmental disorder (6 variants)
- Encephalopathy, progressive, early-onset, with episodic rhabdomyolysis (6 variants)
- Rare genetic intellectual disability (5 variants)
- Developmental disorder (3 variants)
- Autism spectrum disorder (2 variants)
- Abnormality of the nervous system (2 variants)
- Macrocephaly;Global developmental delay;Seizure;Atypical behavior;Hand tremor (1 variants)
- Abnormal facial shape;Seizure;Conductive hearing impairment;Delayed speech and language development;Global developmental delay (1 variants)
- Neurodevelopmental delay (1 variants)
- 8 conditions (1 variants)
- Seizure (1 variants)
- Sudden unexplained death in childhood (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the ANKRD11 gene is commonly pathogenic or not.
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.
Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
---|---|---|---|---|---|---|
synonymous | 441 | 35 | 482 | |||
missense | 22 | 651 | 157 | 29 | 861 | |
nonsense | 88 | 26 | 114 | |||
start loss | 0 | |||||
frameshift | 205 | 57 | 265 | |||
inframe indel | 37 | 40 | ||||
splice donor/acceptor (+/-2bp) | 11 | 17 | ||||
splice region ? | 2 | 13 | 12 | 27 | ||
non coding ? | 14 | 78 | 50 | 144 | ||
Total | 309 | 110 | 713 | 677 | 114 |
Highest pathogenic variant AF is 0.00000658
Variants in ANKRD11
This is a list of pathogenic ClinVar variants found in the ANKRD11 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
16-89268198-G-C | Benign (Apr 04, 2020) | |||
16-89268210-C-T | Benign (Apr 13, 2020) | |||
16-89268213-G-C | Benign (Apr 13, 2020) | |||
16-89268253-G-A | Likely benign (Aug 31, 2020) | |||
16-89268271-G-A | Likely benign (Feb 13, 2020) | |||
16-89268320-G-A | Benign (Aug 31, 2018) | |||
16-89268470-C-T | Benign (Mar 01, 2022) | |||
16-89268491-A-G | Global developmental delay | Uncertain significance (Aug 17, 2022) | ||
16-89268493-T-A | KBG syndrome | Likely benign (May 31, 2023) | ||
16-89268513-C-T | KBG syndrome | Uncertain significance (Apr 20, 2022) | ||
16-89268514-G-A | KBG syndrome | Likely benign (Apr 19, 2022) | ||
16-89268517-C-T | Inborn genetic diseases | Uncertain significance (Jan 16, 2024) | ||
16-89268518-A-G | KBG syndrome | Uncertain significance (Jul 01, 2022) | ||
16-89268525-C-T | Likely pathogenic (Sep 06, 2022) | |||
16-89268526-G-A | Inborn genetic diseases • KBG syndrome | Likely benign (Sep 01, 2022) | ||
16-89268526-G-T | KBG syndrome | Likely pathogenic (Jun 16, 2016) | ||
16-89268527-TAGA-T | Uncertain significance (Oct 27, 2022) | |||
16-89268531-A-AGG | not specified | Uncertain significance (Mar 16, 2022) | ||
16-89268538-C-A | KBG syndrome | Likely benign (May 08, 2022) | ||
16-89268541-C-G | Inborn genetic diseases • KBG syndrome | Uncertain significance (Feb 16, 2023) | ||
16-89268543-C-T | Uncertain significance (May 17, 2018) | |||
16-89268544-G-A | KBG syndrome | Likely benign (Dec 18, 2023) | ||
16-89268549-C-T | Uncertain significance (Jan 11, 2022) | |||
16-89268581-T-TCCTGCACCTTCAGCTGCCACTC | Uncertain significance (Apr 30, 2019) | |||
16-89268583-C-T | Inborn genetic diseases • KBG syndrome | Likely benign (Dec 08, 2022) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
ANKRD11 | protein_coding | protein_coding | ENST00000301030 | 11 | 222932 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
1.00 | 1.69e-11 | 125741 | 0 | 7 | 125748 | 0.0000278 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | -0.554 | 1657 | 1.59e+3 | 1.04 | 0.000114 | 17483 |
Missense in Polyphen | 463 | 660.5 | 0.70098 | 7316 | ||
Synonymous | -7.96 | 1033 | 755 | 1.37 | 0.0000660 | 5171 |
Loss of Function | 8.17 | 4 | 85.5 | 0.0468 | 0.00000496 | 1133 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.0000289 | 0.0000289 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.00 | 0.00 |
Finnish | 0.0000977 | 0.0000924 |
European (Non-Finnish) | 0.0000374 | 0.0000352 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.00 | 0.00 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Chromatin regulator which modulates histone acetylation and gene expression in neural precursor cells (By similarity). May recruit histone deacetylases (HDACs) to the p160 coactivators/nuclear receptor complex to inhibit ligand-dependent transactivation (PubMed:15184363). Has a role in proliferation and development of cortical neural precursors (PubMed:25556659). May also regulate bone homeostasis (By similarity). {ECO:0000250|UniProtKB:E9Q4F7, ECO:0000269|PubMed:15184363, ECO:0000269|PubMed:25556659}.;
- Disease
- DISEASE: KBG syndrome (KBGS) [MIM:148050]: A syndrome characterized by macrodontia of the upper central incisors, distinctive craniofacial findings, short stature, skeletal anomalies, and neurologic involvement that includes global developmental delay, seizures, and intellectual disability. {ECO:0000269|PubMed:21782149, ECO:0000269|PubMed:25413698}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Recessive Scores
- pRec
- 0.107
Intolerance Scores
- loftool
- 0.0131
- rvis_EVS
- -4.38
- rvis_percentile_EVS
- 0.09
Haploinsufficiency Scores
- pHI
- 0.249
- hipred
- Y
- hipred_score
- 0.689
- ghis
- 0.633
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.934
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ankrd11
- Phenotype
- hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); embryo phenotype; skeleton phenotype; immune system phenotype; vision/eye phenotype; hearing/vestibular/ear phenotype; growth/size/body region phenotype; homeostasis/metabolism phenotype; craniofacial phenotype;
Gene ontology
- Biological process
- in utero embryonic development;tissue homeostasis;multicellular organism growth;odontogenesis of dentin-containing tooth;skeletal system morphogenesis;face morphogenesis;bone development
- Cellular component
- nucleus;nucleoplasm;cytosol;plasma membrane
- Molecular function