AKNA

protein-coding

AT-hook transcription factor

Gene summary

Predicted to enable DNA binding activity. Involved in positive regulation of transcription by RNA polymerase II. Located in centrosome; fibrillar center; and nucleoplasm. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001317950.2

Inheritance

ClinVar variants

U:262B:32

Top phenotype

AKNA-related autism spectrum disorder

gnomAD constraint

pLI —, LoF o/e 0.31

Max pathogenic AF

—

Genomic locus

chr9:114,334,156-114,394,405

External References & Databases

Ensembl (ENSG00000106948)

Transcript & Mutation Effects

hg38 • Region Span ~60.2 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

primary ciliary dyskinesiaLIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0016575

Submitter: PanelApp Australia

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to AKNA variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 267

not providedTotal: 18

AKNA-related autism spectrum disorderTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001317950.2. 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	2 clinvar	4 clinvar	10
missense			254 clinvar	22 clinvar	4 clinvar	280
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	262	24	8	294

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 32 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001317950.2	RefSeq	NP_001304879.1	21	MANE Select
ENST00000374088.8	Ensembl	ENSP00000363201.3	21	MANE Select
NM_001317952.1	RefSeq	NP_001304881.1	20	Standard
NM_030767.5	RefSeq	NP_110394.3	21	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

positive regulation of transcription by RNA polymerase II

Molecular Function

RNA polymerase II proximal promoter sequence-specific DNA binding
DNA-binding transcription factor activity, RNA polymerase II-specific
DNA-binding transcription activator activity, RNA polymerase II-specific

Cellular Component

fibrillar center
nucleoplasm
centrosome
cytosol
membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000307564
Coding exons: 21
Length: 60250
Individuals with no LoFs: 125688
Homozygous LoFs: 0
Heterozygous LoFs: 60
Defined: 125748
p: 0.000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.129	835	825	1.01	0.0000487	9171
Missense (PolyPhen)		152	166.21	0.91449		2045
Synonymous	0.0230	342	343	0.998	0.0000209	3097
Loss of Function	5.01	19	61.4	0.309	0.00000319	692

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00063	0.00062	rare
Latino/Admixed American	0.00028	0.00026	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00025	0.00024	rare
South Asian	0.00043	0.00042	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Transcription factor that specifically activates the expression of the CD40 receptor and its ligand CD40L/CD154, two cell surface molecules on lymphocytes that are critical for antigen-dependent-B-cell development. Binds to A/T-rich promoters. {ECO:0000269|PubMed:11268217}.;

Recessive Scores

pRec: 0.0824

Intolerance Scores

LoFtool: 0.706
RVIS EVS: 0.38
RVIS percentile EVS: 75.52

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: N
Indispensability score: 0.0484

Gene Damage Prediction

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