AHDC1
Basic information
Region (hg38): 1:27534034-27604431
Links
Phenotypes
GenCC
Source:
- AHDC1-related intellectual disability - obstructive sleep apnea - mild dysmorphism syndrome (Strong), mode of inheritance: AD
- AHDC1-related intellectual disability - obstructive sleep apnea - mild dysmorphism syndrome (Definitive), mode of inheritance: AD
- AHDC1-related intellectual disability - obstructive sleep apnea - mild dysmorphism syndrome (Strong), mode of inheritance: AD
- AHDC1-related intellectual disability - obstructive sleep apnea - mild dysmorphism syndrome (Supportive), mode of inheritance: AD
- AHDC1-related intellectual disability - obstructive sleep apnea - mild dysmorphism syndrome (Strong), mode of inheritance: AD
- AHDC1-related intellectual disability - obstructive sleep apnea - mild dysmorphism syndrome (Definitive), mode of inheritance: AD
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Xia-Gibbs 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 | Audiologic/Otolaryngologic; Craniofacial; Neurologic | 24791903 |
ClinVar
This is a list of variants' phenotypes submitted to
- not provided (701 variants)
- AHDC1-related intellectual disability - obstructive sleep apnea - mild dysmorphism syndrome (166 variants)
- Inborn genetic diseases (78 variants)
- not specified (16 variants)
- AHDC1-related condition (10 variants)
- See cases (7 variants)
- Neurodevelopmental abnormality (3 variants)
- Sleep apnea;Intellectual disability;Global developmental delay;Delayed speech and language development;Neonatal hypotonia (3 variants)
- Intellectual disability (3 variants)
- Sleep apnea;Delayed speech and language development;Hypotonia (3 variants)
- Neurodevelopmental delay (2 variants)
- Neurodevelopmental disorder (1 variants)
- Autism spectrum disorder (1 variants)
- Spastic ataxia (1 variants)
- Abdominal obesity-metabolic syndrome 3 (1 variants)
- Cerebral visual impairment and intellectual disability (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the AHDC1 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 | 219 | 26 | 248 | |||
missense | 342 | 84 | 13 | 441 | ||
nonsense | 24 | 32 | ||||
start loss | 0 | |||||
frameshift | 54 | 17 | 74 | |||
inframe indel | 10 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region ? | 0 | |||||
non coding ? | 4 | |||||
Total | 78 | 26 | 355 | 308 | 42 |
Variants in AHDC1
This is a list of pathogenic ClinVar variants found in the AHDC1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
1-27547319-G-A | AHDC1-related intellectual disability - obstructive sleep apnea - mild dysmorphism syndrome | Benign/Likely benign (Nov 20, 2023) | ||
1-27547326-G-C | Uncertain significance (Jan 13, 2023) | |||
1-27547334-G-A | AHDC1-related intellectual disability - obstructive sleep apnea - mild dysmorphism syndrome | Benign (Mar 01, 2024) | ||
1-27547347-G-A | Uncertain significance (Oct 03, 2023) | |||
1-27547351-T-C | Uncertain significance (Dec 13, 2023) | |||
1-27547355-C-A | Likely benign (Aug 22, 2022) | |||
1-27547362-A-AAGCC | Uncertain significance (Oct 23, 2023) | |||
1-27547364-G-A | Likely benign (Aug 10, 2022) | |||
1-27547366-C-T | Uncertain significance (Apr 27, 2023) | |||
1-27547367-G-A | Likely benign (Oct 03, 2023) | |||
1-27547377-C-A | Uncertain significance (Dec 01, 2022) | |||
1-27547384-C-T | Uncertain significance (Nov 01, 2022) | |||
1-27547398-G-A | Inborn genetic diseases | Conflicting classifications of pathogenicity (Apr 24, 2023) | ||
1-27547399-C-A | Likely benign (Aug 09, 2022) | |||
1-27547429-C-T | Uncertain significance (Aug 15, 2022) | |||
1-27547430-G-A | Likely benign (May 08, 2022) | |||
1-27547437-T-A | AHDC1-related intellectual disability - obstructive sleep apnea - mild dysmorphism syndrome | Uncertain significance (May 28, 2019) | ||
1-27547442-G-A | Likely benign (Apr 13, 2022) | |||
1-27547449-A-T | Inborn genetic diseases | Uncertain significance (Jun 20, 2023) | ||
1-27547452-G-A | Spastic ataxia • Inborn genetic diseases | Benign/Likely benign (Jan 18, 2024) | ||
1-27547461-G-A | Likely benign (Aug 17, 2023) | |||
1-27547465-C-A | AHDC1-related disorder | Uncertain significance (Jan 03, 2024) | ||
1-27547466-G-A | AHDC1-related disorder | Likely benign (Jan 15, 2024) | ||
1-27547470-G-T | Uncertain significance (Oct 23, 2022) | |||
1-27547474-G-A | Likely benign (Sep 29, 2022) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
AHDC1 | protein_coding | protein_coding | ENST00000374011 | 1 | 70397 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
1.00 | 8.53e-7 | 125148 | 0 | 1 | 125149 | 0.00000400 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 2.86 | 764 | 1.02e+3 | 0.748 | 0.0000727 | 10021 |
Missense in Polyphen | 85 | 120.67 | 0.7044 | 1043 | ||
Synonymous | -0.567 | 488 | 472 | 1.03 | 0.0000351 | 3692 |
Loss of Function | 5.78 | 0 | 38.9 | 0.00 | 0.00000231 | 434 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00 | 0.00 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.0000545 | 0.0000545 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.00 | 0.00 |
Middle Eastern | 0.0000545 | 0.0000545 |
South Asian | 0.00 | 0.00 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Disease
- DISEASE: Mental retardation, autosomal dominant 25 (MRD25) [MIM:615829]: A disorder characterized by significantly below average general intellectual functioning associated with impairments in adaptive behavior and manifested during the developmental period. MRD25 additional features include mild dysmorphism, hypotonia, delayed psychomotor development with absent or poor expressive language, hypoplasia of the corpus callosum, simplified gyral pattern, and delayed myelination. {ECO:0000269|PubMed:24791903}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
- Pathway
- Mesodermal Commitment Pathway
(Consensus)
Intolerance Scores
- loftool
- 0.0110
- rvis_EVS
- -1.1
- rvis_percentile_EVS
- 6.98
Haploinsufficiency Scores
- pHI
- 0.0929
- hipred
- Y
- hipred_score
- 0.675
- ghis
- 0.581
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.526
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ahdc1
- Phenotype
Gene ontology
- Biological process
- Cellular component
- Molecular function
- DNA binding