AHCTF1

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

Basic information

Region (hg38): 1:246839098-246931948

Links

ENSG00000153207

∙ NCBI:25909 ∙ OMIM:610853 ∙ HGNC:24618 ∙ Uniprot:Q8WYP5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

not_specified (265 variants)
not_provided (5 variants)
Strabismus (1 variants)
Intellectual_disability (1 variants)
Delayed_speech_and_language_development (1 variants)

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. These statistics are base on transcript: NM_001323342.2. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				4 clinvar		4
missense			243 clinvar	22 clinvar		265
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	244	26	0

Loading clinvar variants...

GnomAD

Source: gnomAD

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: 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

	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