AHCYL1
adenosylhomocysteinase like 1, the group of Protein phosphatase 1 regulatory subunits
Basic information
Region (hg38): 1:109984765-110023742
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the AHCYL1 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 | 0 | |||||
| missense | 10 | 10 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 10 | 0 | 0 |
Variants in AHCYL1
This is a list of pathogenic ClinVar variants found in the AHCYL1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-109985164-C-T | not specified | Uncertain significance (Jun 01, 2023) | ||
| 1-110009101-T-C | not specified | Uncertain significance (Jan 23, 2024) | ||
| 1-110012967-A-G | not specified | Uncertain significance (Mar 29, 2023) | ||
| 1-110014769-C-T | not specified | Uncertain significance (Nov 01, 2022) | ||
| 1-110014823-G-A | not specified | Uncertain significance (Aug 18, 2023) | ||
| 1-110016345-C-G | not specified | Uncertain significance (Dec 14, 2023) | ||
| 1-110016702-A-G | not specified | Uncertain significance (Aug 16, 2021) | ||
| 1-110018429-G-A | not specified | Uncertain significance (Mar 22, 2023) | ||
| 1-110018453-A-T | not specified | Uncertain significance (Oct 20, 2023) | ||
| 1-110018564-A-G | not specified | Uncertain significance (Aug 29, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| AHCYL1 | protein_coding | protein_coding | ENST00000369799 | 17 | 39050 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.994 | 0.00571 | 125741 | 0 | 6 | 125747 | 0.0000239 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 4.02 | 112 | 312 | 0.359 | 0.0000172 | 3472 |
| Missense in Polyphen | 21 | 114.16 | 0.18396 | 1307 | ||
| Synonymous | 0.248 | 112 | 115 | 0.971 | 0.00000639 | 1002 |
| Loss of Function | 4.91 | 5 | 37.4 | 0.134 | 0.00000220 | 388 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.0000993 | 0.0000992 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000441 | 0.0000439 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Multifaceted cellular regulator which coordinates several essential cellular functions including regulation of epithelial HCO3(-) and fluid secretion, mRNA processing and DNA replication. Regulates ITPR1 sensitivity to inositol 1,4,5- trisphosphate competing for the common binding site and acting as endogenous 'pseudoligand' whose inhibitory activity can be modulated by its phosphorylation status. In the pancreatic and salivary ducts, at resting state, attenuates inositol 1,4,5- trisphosphate-induced calcium release by interacting with ITPR1 (PubMed:16793548). When extracellular stimuli induce ITPR1 phosphorylation or inositol 1,4,5-trisphosphate production, dissociates of ITPR1 to interact with CFTR and SLC26A6 mediating their synergistic activation by calcium and cAMP that stimulates the epithelial secretion of electrolytes and fluid (By similarity). Also activates basolateral SLC4A4 isoform 1 to coordinate fluid and HCO3(-) secretion (PubMed:16769890). Inhibits the effect of STK39 on SLC4A4 and CFTR by recruiting PP1 phosphatase which activates SLC4A4, SLC26A6 and CFTR through dephosphorylation (By similarity). Mediates the induction of SLC9A3 surface expression produced by Angiotensin-2 (PubMed:20584908). Depending on the cell type, activates SLC9A3 in response to calcium or reverses SLC9A3R2-dependent calcium inhibition (PubMed:18829453). May modulate the polyadenylation state of specific mRNAs, both by controlling the subcellular location of FIP1L1 and by inhibiting PAPOLA activity, in response to a stimulus that alters its phosphorylation state (PubMed:19224921). Acts as a (dATP)-dependent inhibitor of ribonucleotide reductase large subunit RRM1, controlling the endogenous dNTP pool and ensuring normal cell cycle progression (PubMed:25237103). In vitro does not exhibit any S-adenosyl-L- homocysteine hydrolase activity (By similarity). {ECO:0000250|UniProtKB:B5DFN2, ECO:0000250|UniProtKB:Q80SW1, ECO:0000269|PubMed:16769890, ECO:0000269|PubMed:16793548, ECO:0000269|PubMed:18829453, ECO:0000269|PubMed:19224921, ECO:0000269|PubMed:20584908, ECO:0000269|PubMed:25237103}.;
- Pathway
- Cysteine and methionine metabolism - Homo sapiens (human);Trans-sulfuration and one carbon metabolism;One carbon metabolism and related pathways;Signaling by GPCR;Antigen activates B Cell Receptor (BCR) leading to generation of second messengers;Signal Transduction;VEGFA-VEGFR2 Pathway;Signaling by the B Cell Receptor (BCR);CLEC7A (Dectin-1) induces NFAT activation;CLEC7A (Dectin-1) signaling;C-type lectin receptors (CLRs);Role of phospholipids in phagocytosis;Fcgamma receptor (FCGR) dependent phagocytosis;methionine degradation;FCERI mediated Ca+2 mobilization;Fc epsilon receptor (FCERI) signaling;Innate Immune System;Immune System;Metabolism;Methionine Cysteine metabolism;Adaptive Immune System;Ion homeostasis;Regulation of insulin secretion;Cardiac conduction;Muscle contraction;Selenoamino acid metabolism;EGFR1;DAG and IP3 signaling;Signaling by VEGF;PLC beta mediated events;G-protein mediated events;Opioid Signalling;G alpha (i) signalling events;cysteine biosynthesis;superpathway of methionine degradation;Signaling by Receptor Tyrosine Kinases;Integration of energy metabolism;GPCR downstream signalling;Intracellular signaling by second messengers;VEGFR2 mediated cell proliferation
(Consensus)
Recessive Scores
- pRec
- 0.191
Intolerance Scores
- loftool
- 0.139
- rvis_EVS
- -0.43
- rvis_percentile_EVS
- 25.15
Haploinsufficiency Scores
- pHI
- 0.355
- hipred
- Y
- hipred_score
- 0.673
- ghis
- 0.632
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.957
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ahcyl1
- Phenotype
- vision/eye phenotype; digestive/alimentary phenotype; skeleton phenotype; pigmentation phenotype; growth/size/body region phenotype; hematopoietic system phenotype; homeostasis/metabolism phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); endocrine/exocrine gland phenotype;
Zebrafish Information Network
- Gene name
- ahcyl1
- Affected structure
- post-vent region
- Phenotype tag
- abnormal
- Phenotype quality
- distended
Gene ontology
- Biological process
- mRNA polyadenylation;protein export from nucleus;one-carbon metabolic process;positive regulation of sodium ion transport;regulation of mRNA 3'-end processing;regulation of ion transmembrane transporter activity;S-adenosylmethionine cycle;angiotensin-activated signaling pathway;epithelial fluid transport;regulation of anion transport;response to calcium ion;regulation of cardiac conduction
- Cellular component
- cytoplasm;endoplasmic reticulum membrane;cytosol;apical plasma membrane;extracellular exosome
- Molecular function
- RNA binding;adenosylhomocysteinase activity;protein binding;identical protein binding