AKNA

AT-hook transcription factor

Basic information

Region (hg38): 9:114334156-114394405

Links

ENSG00000106948 ∙ NCBI:80709 ∙ OMIM:605729 ∙ HGNC:24108 ∙ Uniprot:Q7Z591 ∙ 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 AKNA gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the AKNA 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				2	4	6
missense			100	10	4	114
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	101	12	8

Variants in AKNA

This is a list of pathogenic ClinVar variants found in the AKNA region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
9-114337083-G-A		not specified	Uncertain significance (Nov 01, 2022)
9-114337091-C-T		not specified	Uncertain significance (Feb 28, 2024)
9-114337095-G-T		not specified	Uncertain significance (Oct 24, 2023)
9-114337109-G-A		not specified	Uncertain significance (Sep 14, 2022)
9-114337121-T-C		not specified	Uncertain significance (Aug 02, 2022)
9-114337137-G-A		not specified	Uncertain significance (Mar 23, 2022)
9-114337149-C-T		not specified	Uncertain significance (Jun 02, 2023)
9-114337164-G-A		not specified	Uncertain significance (Feb 22, 2023)
9-114337203-C-T		not specified	Uncertain significance (May 30, 2023)
9-114337217-T-A		not specified	Uncertain significance (Sep 22, 2023)
9-114337238-G-T		not specified	Uncertain significance (Jun 16, 2023)
9-114341587-G-A		not specified	Uncertain significance (Jul 05, 2022)
9-114341647-G-A		not specified	Uncertain significance (May 21, 2024)
9-114341650-G-A		not specified	Uncertain significance (Jun 29, 2023)
9-114341707-G-A		not specified	Uncertain significance (Apr 23, 2024)
9-114342026-G-C		not specified	Uncertain significance (Jun 11, 2021)
9-114342050-C-A		not specified	Uncertain significance (Jan 30, 2024)
9-114342050-C-T		not specified	Uncertain significance (Feb 07, 2023)
9-114342060-C-T		not specified	Uncertain significance (Jul 08, 2021)
9-114343713-T-A		not specified	Uncertain significance (May 13, 2024)
9-114345917-C-G		not specified	Uncertain significance (Aug 04, 2021)
9-114345940-T-C		not specified	Uncertain significance (Oct 06, 2021)
9-114346716-C-T		not specified	Uncertain significance (Oct 25, 2023)
9-114347730-T-C		not specified	Uncertain significance (May 04, 2022)
9-114347745-G-A		not specified	Uncertain significance (Sep 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
AKNA	protein_coding	protein_coding	ENST00000307564	21	60250

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000129	1.00	125688	0	60	125748	0.000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.129	835	825	1.01	0.0000487	9171
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000912	0.000893
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000464	0.0000462
European (Non-Finnish)	0.000249	0.000237
Middle Eastern	0.00	0.00
South Asian	0.000428	0.000425
Other	0.00	0.00

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.0634
• hipred: N
• hipred_score: 0.233
• ghis: 0.543

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0484

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Akna
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system 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); hematopoietic system phenotype; immune system phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: positive regulation of transcription by RNA polymerase II
• Cellular component: fibrillar center;nucleoplasm;centrosome;cytosol;membrane;intracellular membrane-bounded organelle
• 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