AHCTF1

AT-hook containing transcription factor 1, the group of Nucleoporins

Basic information

Region (hg38): 1:246839098-246931948

Links

ENSG00000153207NCBI:25909OMIM:610853HGNC:24618Uniprot:Q8WYP5AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the AHCTF1 gene.

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
clinvar
3
missense
97
clinvar
14
clinvar
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)2524467
1-246840905-T-G not specified Uncertain significance (Jun 23, 2021)2232998
1-246840937-A-C not specified Uncertain significance (Aug 17, 2021)2246416
1-246840984-T-C not specified Uncertain significance (Dec 16, 2023)3097899
1-246840988-T-C not specified Uncertain significance (Oct 06, 2021)2221402
1-246843863-T-C not specified Uncertain significance (Feb 21, 2024)3097893
1-246849707-C-T not specified Uncertain significance (Mar 18, 2024)3276888
1-246849744-C-T not specified Uncertain significance (Oct 06, 2022)2317429
1-246849804-G-A not specified Uncertain significance (Dec 20, 2021)2402382
1-246849848-T-C not specified Uncertain significance (Nov 01, 2022)2321792
1-246849891-A-T not specified Uncertain significance (Jan 19, 2024)3097884
1-246849950-T-C not specified Uncertain significance (Jun 17, 2022)2295542
1-246849956-C-A not specified Uncertain significance (May 17, 2023)2507942
1-246849978-T-C not specified Uncertain significance (Apr 26, 2023)2540940
1-246849990-T-C not specified Uncertain significance (Jun 29, 2023)2608547
1-246850020-T-G not specified Uncertain significance (May 11, 2022)2372411
1-246850086-G-A not specified Uncertain significance (Aug 22, 2023)2599094
1-246850106-A-G not specified Likely benign (Feb 15, 2023)2461250
1-246850122-G-C not specified Uncertain significance (Mar 29, 2022)2280699
1-246850179-C-T not specified Uncertain significance (Feb 07, 2023)2481469
1-246850205-T-C not specified Likely benign (Dec 03, 2021)2221409
1-246850214-C-T not specified Uncertain significance (Jul 05, 2023)2610122
1-246850241-T-C Likely benign (Jan 01, 2023)2640237
1-246850247-T-G not specified Uncertain significance (Sep 16, 2021)2394132
1-246850260-T-G not specified Uncertain significance (Feb 09, 2022)2382785

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
AHCTF1protein_codingprotein_codingENST00000326225 3692881
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
1.006.01e-1312558001621257420.000644
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.38111761.14e+31.030.000057914749
Missense in Polyphen223283.820.785713738
Synonymous-0.1184154121.010.00002134451
Loss of Function9.1181120.07140.000006031454

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0006730.000645
Ashkenazi Jewish0.0002070.000198
East Asian0.0001110.000109
Finnish0.0003780.000370
European (Non-Finnish)0.001020.000941
Middle Eastern0.0001110.000109
South Asian0.0008770.000784
Other0.0006970.000652

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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