AHCTF1

protein-coding

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

Gene summary

Predicted to enable DNA binding activity. Involved in nuclear pore complex assembly and regulation of cytokinesis. Located in chromosome; nuclear body; and nuclear envelope. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001323342.2

Inheritance

—

ClinVar variants

U:304B:29

Top phenotype

Strabismus

gnomAD constraint

pLI —, LoF o/e 0.07

Max pathogenic AF

—

Genomic locus

chr1:246,839,098-246,931,948

External References & Databases

Ensembl (ENSG00000153207)

Transcript & Mutation Effects

hg38 • Region Span ~92.9 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to AHCTF1 variants in ClinVar

5 Conditions Cataloged

not specifiedTotal: 305

not providedTotal: 7

StrabismusTotal: 1

Intellectual disabilityTotal: 1

Delayed speech and language developmentTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001323342.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			4 clinvar	4 clinvar		8
missense			289 clinvar	25 clinvar		314
nonsense			3 clinvar			3
start loss						0
frameshift			3 clinvar			3
splice donor/acceptor (+/-2bp)			5 clinvar			5
Total	0	0	304	29	0	333

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 27 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001323342.2	RefSeq	NP_001310271.1	35	MANE Select
ENST00000648844.2	Ensembl	ENSP00000497061.2	35	MANE Select
NM_001323343.2	RefSeq	NP_001310272.1	35	Standard
NM_001410950.1	RefSeq	NP_001397879.1	36	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
ahctf1	Danio rerio	Structure: retinal ganglion cell Quality: decreased amount abnormal

Gene / Model

Organism

Observed Phenotype

ahctf1

Danio rerio

Structure: retinal ganglion cell

Quality: decreased amount

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

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

Biological Process

regulation of transcription by RNA polymerase II
cell cycle
protein transport
regulation of cytokinesis
mRNA transport

Molecular Function

DNA-binding transcription factor activity, RNA polymerase II-specific
DNA binding

Cellular Component

condensed chromosome kinetochore
chromatin
nucleus
nuclear pore
nucleoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000326225
Coding exons: 36
Length: 92881
Individuals with no LoFs: 125580
Homozygous LoFs: 0
Heterozygous LoFs: 162
Defined: 125742
p: 0.000644

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.381	1176	1.14e+3	1.03	0.0000579	14749
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00040	0.00037	rare
Latino/Admixed American	0.00028	0.00026	rare
Ashkenazi Jewish	0.00021	0.00020	rare
East Asian	0.00011	0.00011	rare
Finnish	0.00038	0.00037	rare
European (Non-Finnish)	0.0010	0.00094	notable
South Asian	0.00088	0.00078	rare
Other	0.00070	0.00065	rare

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.0947

Intolerance Scores

LoFtool: 0.233
RVIS EVS: 0.54
RVIS percentile EVS: 81.02

Essentials

Essential (CRISPR): E
Essential (CRISPR2): S
Essential (gene trap): E
Indispensability pred.: N
Indispensability score: 0.294

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium