AKNAD1

Summary

AKNAD1 (AKNA domain containing 1, HGNC:28398) is a protein-coding gene on chromosome 1p13.3, encoding Protein AKNAD1 (Q5T1N1).

This gene encodes a protein which contains a domain found in an AT-hook-containing transcription factor. Alternative splicing results in multiple transcript variants.

Source: NCBI Gene 254268 — RefSeq curated summary.

At a glance

• GWAS associations: 5
• Clinical variants (ClinVar): 148 total
• MANE Select transcript: NM_152763

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28398
Approved symbol	AKNAD1
Name	AKNA domain containing 1
Location	1p13.3
Locus type	gene with protein product
Status	Approved
Aliases	MGC26989
Ensembl gene	ENSG00000162641
Ensembl biotype	protein_coding
OMIM	621318
Entrez	254268

Gene structure

Transcript identifiers

Ensembl transcripts: 10 — 4 protein_coding, 3 nonsense_mediated_decay, 2 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000357393, ENST00000369994, ENST00000369995, ENST00000370001, ENST00000461774, ENST00000466413, ENST00000472781, ENST00000474186, ENST00000477908, ENST00000603450

RefSeq mRNA: 1 — MANE Select: NM_152763 NM_152763

CCDS: CCDS791

Canonical transcript exons

ENST00000370001 — 16 exons

Exon	Start	End
ENSE00001067205	108837550	108837706
ENSE00001212297	108856929	108857094
ENSE00001409796	108834447	108834528
ENSE00001410376	108834929	108835056
ENSE00001734794	108820545	108820626
ENSE00002035173	108823370	108823477
ENSE00002157363	108851672	108852767
ENSE00003503900	108827205	108827302
ENSE00003504237	108830559	108830650
ENSE00003589473	108815901	108816302
ENSE00003641275	108817048	108817177
ENSE00003671833	108823566	108823688
ENSE00003860251	108849537	108849576
ENSE00003871950	108848912	108849060
ENSE00003872560	108848752	108848814
ENSE00003885197	108843134	108843267

Expression profiles

Bgee: expression breadth ubiquitous, 155 present calls, max score 94.98.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0409 / max 15.5008, expressed in 13 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
13662	23.7284	1818
13659	0.0211	8
13658	0.0127	6
13657	0.0071	3

Top tissues by expression

238 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
buccal mucosa cell	CL:0002336	94.98	silver quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	86.34	gold quality
right testis	UBERON:0004534	75.88	gold quality
left testis	UBERON:0004533	75.85	gold quality
calcaneal tendon	UBERON:0003701	75.84	gold quality
testis	UBERON:0000473	74.03	gold quality
mucosa of stomach	UBERON:0001199	69.94	gold quality
lower esophagus muscularis layer	UBERON:0035833	69.92	gold quality
lower esophagus	UBERON:0013473	69.86	gold quality
sperm	CL:0000019	69.30	gold quality
tendon	UBERON:0000043	68.93	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	68.38	gold quality
lower esophagus mucosa	UBERON:0035834	68.18	gold quality
ganglionic eminence	UBERON:0004023	68.05	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	66.05	gold quality
ectocervix	UBERON:0012249	65.94	gold quality
esophagus	UBERON:0001043	64.45	gold quality
right adrenal gland cortex	UBERON:0035827	64.20	gold quality
spinal cord	UBERON:0002240	63.71	gold quality
tibial nerve	UBERON:0001323	63.50	gold quality
skin of abdomen	UBERON:0001416	62.86	gold quality
skin of leg	UBERON:0001511	62.69	gold quality
smooth muscle tissue	UBERON:0001135	62.62	gold quality
body of uterus	UBERON:0009853	62.18	gold quality
left uterine tube	UBERON:0001303	61.24	gold quality
left adrenal gland	UBERON:0001234	60.91	gold quality
right adrenal gland	UBERON:0001233	60.71	gold quality
muscle layer of sigmoid colon	UBERON:0035805	60.71	gold quality
esophagus mucosa	UBERON:0002469	60.59	gold quality
zone of skin	UBERON:0000014	60.16	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	4.94

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

22 targeting AKNAD1, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-3658	99.96	73.87	4379
HSA-MIR-6508-5P	99.92	70.67	2465
HSA-MIR-3140-3P	99.88	68.47	2069
HSA-MIR-8067	99.86	69.59	2260
HSA-MIR-2052	99.79	69.37	2031
HSA-MIR-7856-5P	99.75	69.99	2901
HSA-MIR-6751-5P	99.56	64.99	1145
HSA-MIR-1275	99.47	67.90	2749
HSA-MIR-5009-3P	99.45	69.43	1341
HSA-MIR-6507-5P	99.36	70.46	2524
HSA-MIR-6803-5P	99.19	63.90	1026
HSA-MIR-7109-5P	99.18	66.13	1057
HSA-MIR-625-5P	99.02	68.64	2031
HSA-MIR-4424	98.91	70.33	1145
HSA-MIR-4684-5P	98.29	67.99	1650
HSA-MIR-660-5P	98.16	68.27	680
HSA-MIR-4665-5P	97.91	67.69	1536
HSA-MIR-517-5P	97.13	68.43	781
HSA-MIR-3059-3P	96.71	67.08	606
HSA-MIR-5591-3P	96.23	67.03	489
HSA-MIR-584-5P	95.82	68.05	848
HSA-MIR-1251-5P	95.78	64.10	374

Literature-anchored findings (GeneRIF, showing 1)

• a significant copy number variation in gene AKNAD1 associated with type-2 diabetes, was identified and experimentally validated. (PMID:26292654)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	akna	ENSDARG00000087110
mus_musculus	Aknad1	ENSMUSG00000049565
rattus_norvegicus	Aknad1	ENSRNOG00000028025

Paralogs (1): AKNA (ENSG00000106948)

Protein

Protein identifiers

Protein AKNAD1 — Q5T1N1 (reviewed: Q5T1N1)

All UniProt accessions (4): Q5T1N1, F2Z2Q7, F8W8V4, Q5T1N2

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the AKNA family.

Isoforms (4)

UniProt ID	Names	Canonical?
Q5T1N1-1	1	yes
Q5T1N1-2	2
Q5T1N1-3	3
Q5T1N1-4	4

RefSeq proteins (1): NP_689976* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR022150	AKNA_dom	Domain
IPR052655	AKNA_Centrosome-Trans_reg	Family

Pfam: PF12443

UniProt features (27 total): sequence variant 8, splice variant 5, region of interest 4, sequence conflict 4, compositionally biased region 4, chain 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5T1N1-F1	49.77	0.08

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 35 (showing top): RAY_TUMORIGENESIS_BY_ERBB2_CDC25A_UP, ZHOU_INFLAMMATORY_RESPONSE_LIVE_UP, AR_Q6, GREB1_TARGET_GENES, NFE2L1_TARGET_GENES, TFEB_TARGET_GENES, UBN1_TARGET_GENES, ZNF362_TARGET_GENES, MIR3658, MIR1275, MIR2052, MIR3140_3P, MIR4665_5P, MIR517_5P, AHRR_TARGET_GENES

GO Biological Process (0):

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1

Protein interactions and networks

STRING

1522 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
AKNAD1	CTXND1	A0A1B0GTU2	520
AKNAD1	PARM1	Q6UWI2	489
AKNAD1	CLCC1	Q96S66	478
AKNAD1	EEIG2	Q5T8I3	464
AKNAD1	TMEM167B	Q9NRX6	456
AKNAD1	CFAP276	Q5T5A4	438
AKNAD1	CSDC2	Q9Y534	417
AKNAD1	GPSM2	P81274	399
AKNAD1	TMEM266	Q2M3C6	397
AKNAD1	TECRL	Q5HYJ1	393
AKNAD1	WDR47	O94967	389
AKNAD1	SPATS2L	Q9NUQ6	367
AKNAD1	STXBP3	O00186	365
AKNAD1	SLC35A3	Q9Y2D2	359
AKNAD1	HMSD	A8MTL9	353

IntAct

4 interactions, top by confidence:

A	B	Type	Score
AKNAD1	DTNBP1	psi-mi:“MI:0915”(physical association)	0.400
AKNAD1	NOS1AP	psi-mi:“MI:0915”(physical association)	0.370
AKNAD1	CST4	psi-mi:“MI:0914”(association)	0.350

BioGRID (14): AKNAD1 (Two-hybrid), DTNBP1 (Affinity Capture-MS), GTF2IRD1 (Affinity Capture-MS), AKNAD1 (Two-hybrid), DTNBP1 (Affinity Capture-MS), CST4 (Affinity Capture-MS), CST2 (Affinity Capture-MS), AMY1C (Affinity Capture-MS), SFSWAP (Affinity Capture-MS), CST1 (Affinity Capture-MS), CHD4 (Cross-Linking-MS (XL-MS)), EEA1 (Cross-Linking-MS (XL-MS)), AKNAD1 (Affinity Capture-RNA), APP (Reconstituted Complex)

ESM2 similar proteins: A0A087WRU1, A0JNH1, A2RUB1, A6QNQ6, B0S6S9, B1WC58, D3Z987, D3ZJ47, E1BC15, O60673, P28358, P28359, P56716, P70347, Q0P5X5, Q0VAV2, Q0VBV7, Q15468, Q2M2Z5, Q3UXL4, Q3V089, Q49A88, Q569L8, Q5BQN8, Q5CZC0, Q5QGS0, Q5T1N1, Q5VWN6, Q60988, Q61493, Q62924, Q6ZP01, Q6ZU52, Q6ZVD7, Q80U59, Q80WQ8, Q86WS4, Q86YC2, Q8CB14, Q8IUR6

Diamond homologs: Q5T1N1, Q8WP21, Q7Z591

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

148 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	120
Likely benign	15
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

8618 predictions. Top by Δscore:

Variant	Effect	Δscore
1:108827203:A:AC	donor_gain	1.0000
1:108827204:C:CC	donor_gain	1.0000
1:108837702:CTTTT:C	acceptor_gain	1.0000
1:108848751:CCAG:C	donor_gain	1.0000
1:108856927:AC:A	donor_gain	1.0000
1:108856928:CC:C	donor_gain	1.0000
1:108856934:G:C	donor_gain	1.0000
1:108856949:T:TA	donor_gain	1.0000
1:108856982:C:A	donor_gain	1.0000
1:108896862:A:AG	acceptor_gain	1.0000
1:108896863:G:GG	acceptor_gain	1.0000
1:108896863:GA:G	acceptor_gain	1.0000
1:108897480:T:A	acceptor_gain	1.0000
1:108897629:T:G	donor_loss	1.0000
1:108897954:TTTA:T	acceptor_loss	1.0000
1:108897955:TTAGG:T	acceptor_loss	1.0000
1:108897956:TAGG:T	acceptor_loss	1.0000
1:108897957:A:AT	acceptor_loss	1.0000
1:108898099:TGA:T	donor_gain	1.0000
1:108898099:TGAG:T	donor_loss	1.0000
1:108898100:GA:G	donor_gain	1.0000
1:108898100:GAG:G	donor_gain	1.0000
1:108898101:AG:A	donor_loss	1.0000
1:108898102:G:GG	donor_gain	1.0000
1:108898103:TGA:T	donor_loss	1.0000
1:108898104:GAGTA:G	donor_loss	1.0000
1:108898105:AGT:A	donor_loss	1.0000
1:108898878:GC:G	acceptor_gain	1.0000
1:108898993:AAGT:A	donor_loss	1.0000
1:108898995:G:T	donor_loss	1.0000

AlphaMissense

5549 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:108848922:A:G	L391P	0.979
1:108816266:C:G	A806P	0.977
1:108848803:A:C	F398L	0.954
1:108848803:A:T	F398L	0.954
1:108848805:A:G	F398L	0.954
1:108837685:G:C	F467L	0.951
1:108837685:G:T	F467L	0.951
1:108837687:A:G	F467L	0.951
1:108843242:A:G	L424P	0.950
1:108816211:A:G	L824P	0.940
1:108816256:A:G	L809S	0.938
1:108816278:C:G	A802P	0.938
1:108816221:C:G	A821P	0.936
1:108843254:A:G	L420P	0.936
1:108848804:A:G	F398S	0.934
1:108816274:A:G	L803P	0.931
1:108848943:A:G	L384S	0.924
1:108816252:T:A	K810N	0.922
1:108816252:T:G	K810N	0.922
1:108823473:A:C	F688L	0.922
1:108823473:A:T	F688L	0.922
1:108823475:A:G	F688L	0.922
1:108816234:C:A	M816I	0.921
1:108816234:C:G	M816I	0.921
1:108816234:C:T	M816I	0.921
1:108816253:T:A	K810I	0.908
1:108837668:A:G	L473P	0.907
1:108843145:A:C	F456L	0.904
1:108843145:A:T	F456L	0.904
1:108843147:A:G	F456L	0.904

dbSNP variants (sampled 300 via entrez): RS1000006186 (1:108840333 T>C), RS1000025405 (1:108839861 A>C), RS1000058441 (1:108858370 C>A), RS1000100889 (1:108859490 T>TA), RS1000203576 (1:108843299 A>G), RS1000238220 (1:108834010 G>A,C), RS1000298335 (1:108827771 G>A), RS1000480470 (1:108821781 C>T), RS1000569009 (1:108833688 A>T), RS1000610319 (1:108841744 C>T), RS1000620515 (1:108815743 T>C), RS1000661282 (1:108856828 C>T), RS1000745035 (1:108851313 G>A), RS1000818691 (1:108829229 G>A,C), RS1000836237 (1:108836999 A>C)

Disease associations

OMIM: gene MIM:621318 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

5 associations (top):

Study	Trait	p-value
GCST001343_2	Fat distribution (HIV)	5.000000e-06
GCST001343_5	Fat distribution (HIV)	1.000000e-06
GCST001343_8	Fat distribution (HIV)	4.000000e-06
GCST002004_1	Adverse response to chemotherapy (neutropenia/leucopenia) (carboplatin)	9.000000e-06
GCST010245_72	LDL cholesterol levels	6.000000e-10

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0004341	body fat distribution
EFO:0004611	low density lipoprotein cholesterol measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

16 total (human), top 16 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
aristolochic acid I	increases expression	1
methylmercuric chloride	increases expression	1
bisphenol A	affects cotreatment, decreases methylation	1
sodium arsenate	increases expression, increases abundance	1
sodium arsenite	decreases expression	1
S-(1,2-dichlorovinyl)cysteine	affects response to substance, increases expression	1
tebuconazole	decreases expression	1
abrine	increases expression	1
(+)-JQ1 compound	decreases expression	1
Fulvestrant	affects cotreatment, decreases methylation	1
Arsenic	increases abundance, increases expression	1
Benzo(a)pyrene	decreases methylation	1
Endosulfan	increases expression	1
Folic Acid	increases expression	1
Lipopolysaccharides	decreases expression, affects response to substance, increases expression	1
Smoke	increases expression	1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.