AHCTF1
Basic information
Region (hg38): 1:246839098-246931948
Links
Phenotypes
GenCC
Source:
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 AHCTF1 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 | 3 | |||||
missense | 97 | 14 | 111 | |||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 1 | 1 | ||||
non coding | 0 | |||||
Total | 0 | 0 | 97 | 17 | 0 |
Variants in AHCTF1
This is a list of pathogenic ClinVar variants found in the AHCTF1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
1-246840823-G-A | not specified | Uncertain significance (May 17, 2023) | ||
1-246840905-T-G | not specified | Uncertain significance (Jun 23, 2021) | ||
1-246840937-A-C | not specified | Uncertain significance (Aug 17, 2021) | ||
1-246840984-T-C | not specified | Uncertain significance (Dec 16, 2023) | ||
1-246840988-T-C | not specified | Uncertain significance (Oct 06, 2021) | ||
1-246843863-T-C | not specified | Uncertain significance (Feb 21, 2024) | ||
1-246849707-C-T | not specified | Uncertain significance (Mar 18, 2024) | ||
1-246849744-C-T | not specified | Uncertain significance (Oct 06, 2022) | ||
1-246849804-G-A | not specified | Uncertain significance (Dec 20, 2021) | ||
1-246849848-T-C | not specified | Uncertain significance (Nov 01, 2022) | ||
1-246849891-A-T | not specified | Uncertain significance (Jan 19, 2024) | ||
1-246849950-T-C | not specified | Uncertain significance (Jun 17, 2022) | ||
1-246849956-C-A | not specified | Uncertain significance (May 17, 2023) | ||
1-246849978-T-C | not specified | Uncertain significance (Apr 26, 2023) | ||
1-246849990-T-C | not specified | Uncertain significance (Jun 29, 2023) | ||
1-246850020-T-G | not specified | Uncertain significance (May 11, 2022) | ||
1-246850086-G-A | not specified | Uncertain significance (Aug 22, 2023) | ||
1-246850106-A-G | not specified | Likely benign (Feb 15, 2023) | ||
1-246850122-G-C | not specified | Uncertain significance (Mar 29, 2022) | ||
1-246850179-C-T | not specified | Uncertain significance (Feb 07, 2023) | ||
1-246850205-T-C | not specified | Likely benign (Dec 03, 2021) | ||
1-246850214-C-T | not specified | Uncertain significance (Jul 05, 2023) | ||
1-246850241-T-C | Likely benign (Jan 01, 2023) | |||
1-246850247-T-G | not specified | Uncertain significance (Sep 16, 2021) | ||
1-246850260-T-G | not specified | Uncertain significance (Feb 09, 2022) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
AHCTF1 | protein_coding | protein_coding | ENST00000326225 | 36 | 92881 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
1.00 | 6.01e-13 | 125580 | 0 | 162 | 125742 | 0.000644 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | -0.381 | 1176 | 1.14e+3 | 1.03 | 0.0000579 | 14749 |
Missense in Polyphen | 223 | 283.82 | 0.78571 | 3738 | ||
Synonymous | -0.118 | 415 | 412 | 1.01 | 0.0000213 | 4451 |
Loss of Function | 9.11 | 8 | 112 | 0.0714 | 0.00000603 | 1454 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000673 | 0.000645 |
Ashkenazi Jewish | 0.000207 | 0.000198 |
East Asian | 0.000111 | 0.000109 |
Finnish | 0.000378 | 0.000370 |
European (Non-Finnish) | 0.00102 | 0.000941 |
Middle Eastern | 0.000111 | 0.000109 |
South Asian | 0.000877 | 0.000784 |
Other | 0.000697 | 0.000652 |
dbNSFP
Source:
- Function
- FUNCTION: Required for the assembly of a functional nuclear pore complex (NPC) on the surface of chromosomes as nuclei form at the end of mitosis. May initiate NPC assembly by binding to chromatin and recruiting the Nup107-160 subcomplex of the NPC. Also required for the localization of the Nup107-160 subcomplex of the NPC to the kinetochore during mitosis and for the completion of cytokinesis. {ECO:0000269|PubMed:17098863, ECO:0000269|PubMed:17235358}.;
- Pathway
- Gastric Cancer Network 2;Signal Transduction;Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal;Amplification of signal from the kinetochores;Mitotic Spindle Checkpoint;Cell Cycle Checkpoints;RHO GTPases Activate Formins;RHO GTPase Effectors;Signaling by Rho GTPases;Mitotic Prometaphase;Separation of Sister Chromatids;Mitotic Anaphase;Mitotic Metaphase and Anaphase;M Phase;Cell Cycle;Resolution of Sister Chromatid Cohesion;Cell Cycle, Mitotic
(Consensus)
Recessive Scores
- pRec
- 0.0947
Intolerance Scores
- loftool
- 0.233
- rvis_EVS
- 0.54
- rvis_percentile_EVS
- 81.02
Haploinsufficiency Scores
- pHI
- hipred
- Y
- hipred_score
- 0.515
- ghis
- 0.543
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.294
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ahctf1
- Phenotype
- cellular 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); embryo phenotype;
Zebrafish Information Network
- Gene name
- ahctf1
- Affected structure
- retinal ganglion cell
- Phenotype tag
- abnormal
- Phenotype quality
- decreased amount
Gene ontology
- Biological process
- regulation of transcription by RNA polymerase II;cell cycle;protein transport;regulation of cytokinesis;mRNA transport;nuclear pore complex assembly;cell division
- Cellular component
- condensed chromosome kinetochore;chromatin;nucleus;nuclear pore;nucleoplasm;cytosol;nuclear matrix;nuclear pore outer ring;nuclear membrane;extracellular exosome
- Molecular function
- DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding