KIAA0408

Summary

KIAA0408 (HGNC:21636) is a protein-coding gene on chromosome 6q22.33, encoding Uncharacterized protein KIAA0408 (Q6ZU52).

At a glance

• GWAS associations: 14
• Clinical variants (ClinVar): 105 total
• MANE Select transcript: NM_014702

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:21636
Approved symbol	KIAA0408
Name	KIAA0408
Location	6q22.33
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000189367
Ensembl biotype	protein_coding
OMIM	619236
Entrez	9729

Gene structure

Transcript identifiers

Ensembl transcripts: 11 — 9 protein_coding, 2 retained_intron

ENST00000368281, ENST00000465254, ENST00000472335, ENST00000483725, ENST00000487331, ENST00000906213, ENST00000906214, ENST00000930773, ENST00000947489, ENST00000947490, ENST00000947491

RefSeq mRNA: 1 — MANE Select: NM_014702 NM_014702

CCDS: CCDS34531

Canonical transcript exons

ENST00000483725 — 6 exons

Exon	Start	End
ENSE00001830600	127459175	127459389
ENSE00001935954	127438406	127444282
ENSE00003533277	127449990	127450352
ENSE00003553677	127446408	127447740
ENSE00003604171	127453847	127454101
ENSE00003664602	127449822	127449901

Expression profiles

Bgee: expression breadth ubiquitous, 132 present calls, max score 98.74.

FANTOM5 (CAGE): breadth broad, TPM avg 0.7502 / max 44.8090, expressed in 207 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
75432	0.5125	138
75430	0.1008	55
75433	0.0925	47
75431	0.0444	27

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
cortical plate	UBERON:0005343	98.74	gold quality
ganglionic eminence	UBERON:0004023	97.95	gold quality
ventricular zone	UBERON:0003053	95.47	gold quality
superior frontal gyrus	UBERON:0002661	92.53	gold quality
skeletal muscle tissue	UBERON:0001134	92.17	gold quality
corpus callosum	UBERON:0002336	91.90	gold quality
prefrontal cortex	UBERON:0000451	91.25	gold quality
Brodmann (1909) area 9	UBERON:0013540	91.09	gold quality
primary visual cortex	UBERON:0002436	90.75	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	90.56	gold quality
cerebellar cortex	UBERON:0002129	90.54	gold quality
cerebellar hemisphere	UBERON:0002245	90.52	gold quality
cerebellum	UBERON:0002037	90.35	gold quality
frontal cortex	UBERON:0001870	90.00	gold quality
right hemisphere of cerebellum	UBERON:0014890	89.83	gold quality
cerebral cortex	UBERON:0000956	89.78	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	89.75	gold quality
substantia nigra	UBERON:0002038	88.49	gold quality
anterior cingulate cortex	UBERON:0009835	88.39	gold quality
right frontal lobe	UBERON:0002810	88.02	gold quality
brain	UBERON:0000955	87.93	gold quality
Ammon’s horn	UBERON:0001954	87.89	gold quality
hypothalamus	UBERON:0001898	87.76	gold quality
amygdala	UBERON:0001876	87.24	gold quality
temporal lobe	UBERON:0001871	87.07	gold quality
muscle tissue	UBERON:0002385	87.00	gold quality
calcaneal tendon	UBERON:0003701	86.79	gold quality
hindlimb stylopod muscle	UBERON:0004252	86.56	gold quality
muscle of leg	UBERON:0001383	85.40	gold quality
nucleus accumbens	UBERON:0001882	85.36	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.80

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

277 targeting KIAA0408, 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-3163	100.00	77.23	8605
HSA-LET-7A-3P	100.00	74.03	3932
HSA-LET-7B-3P	100.00	74.08	3913
HSA-LET-7F-1-3P	100.00	74.02	3928
HSA-MIR-98-3P	100.00	74.08	3907
HSA-MIR-30A-5P	100.00	76.31	3233
HSA-MIR-30B-5P	100.00	76.29	3248
HSA-MIR-30C-5P	100.00	76.29	3248
HSA-MIR-30D-5P	100.00	76.32	3233
HSA-MIR-30E-5P	100.00	76.32	3242
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-8485	100.00	77.57	4731
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-1252-5P	100.00	69.80	2774
HSA-MIR-5692B	100.00	71.32	2622
HSA-MIR-5692C	100.00	71.32	2622
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-3134	100.00	66.43	777
HSA-MIR-6856-5P	100.00	65.47	1298
HSA-MIR-3689D	100.00	66.14	1181
HSA-MIR-6851-5P	100.00	65.63	1294
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-6758-5P	100.00	66.21	1470
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-4534	99.99	66.58	1907
HSA-MIR-548AW	99.99	72.57	3559

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	9330159F19Rik	ENSMUSG00000004360
rattus_norvegicus	Kiaa0408L	ENSRNOG00000042309

Protein

Protein identifiers

Uncharacterized protein KIAA0408 — Q6ZU52 (reviewed: Q6ZU52)

All UniProt accessions (3): E9PQS0, H0YEM8, Q6ZU52

Isoforms (2)

UniProt ID	Names	Canonical?
Q6ZU52-1	1	yes
Q6ZU52-2	2

RefSeq proteins (1): NP_055517* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR027882	SOGA1/2-like_CC	Domain

Pfam: PF14818

UniProt features (11 total): region of interest 3, compositionally biased region 3, sequence variant 2, chain 1, coiled-coil region 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6ZU52-F1	52.33	0.10

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 101 (showing top): GTGTTGA_MIR505, TGTTTAC_MIR30A5P_MIR30C_MIR30D_MIR30B_MIR30E5P, DOUGLAS_BMI1_TARGETS_UP, TGCCTTA_MIR124A, YAGI_AML_WITH_T_9_11_TRANSLOCATION, GOTTWEIN_TARGETS_OF_KSHV_MIR_K12_11, chr6q22, CAGTGTT_MIR141_MIR200A, CHENG_IMPRINTED_BY_ESTRADIOL, ALK_DN.V1_DN, GLI4_TARGET_GENES, ZNF350_TARGET_GENES, MIR153_5P, MIR8485, MIR3662

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

422 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
KIAA0408	ABI3	Q9P2A4	651
KIAA0408	ZNF628	Q5EBL2	576
KIAA0408	MTCL3	Q5TF21	570
KIAA0408	ZNF491	Q8N8L2	475
KIAA0408	MMACHC	Q9Y4U1	475
KIAA0408	C6orf58	Q6P5S2	461
KIAA0408	ABHD18	Q0P651	445
KIAA0408	ZNF84	P51523	442
KIAA0408	MANEAL	Q5VSG8	434
KIAA0408	PTPRK	Q15262	432
KIAA0408	ZBED6	P86452	418
KIAA0408	A6NDT3	A6NDT3	417
KIAA0408	PLEKHH1	Q9ULM0	416
KIAA0408	AMZ1	Q400G9	409
KIAA0408	THEMIS	Q8N1K5	404

IntAct

138 interactions, top by confidence:

A	B	Type	Score
KIAA0408	GFAP	psi-mi:“MI:0915”(physical association)	0.740
GFAP	KIAA0408	psi-mi:“MI:0915”(physical association)	0.740
KIAA0408	SORBS3	psi-mi:“MI:0915”(physical association)	0.670
SORBS3	KIAA0408	psi-mi:“MI:0915”(physical association)	0.670
KIAA0408	ABI3	psi-mi:“MI:0915”(physical association)	0.670
KIAA0408	VIM	psi-mi:“MI:0915”(physical association)	0.670
VIM	KIAA0408	psi-mi:“MI:0915”(physical association)	0.670
PHF1	KIAA0408	psi-mi:“MI:0915”(physical association)	0.600
KIAA0408	POLR3C	psi-mi:“MI:0915”(physical association)	0.600
POLR3C	KIAA0408	psi-mi:“MI:0915”(physical association)	0.600
GRB2	KIAA0408	psi-mi:“MI:0915”(physical association)	0.560
NCK2	KIAA0408	psi-mi:“MI:0915”(physical association)	0.560
HSF2BP	KIAA0408	psi-mi:“MI:0915”(physical association)	0.560
KIAA0408	CBY2	psi-mi:“MI:0915”(physical association)	0.560
RUNX1T1	KIAA0408	psi-mi:“MI:0915”(physical association)	0.560
MYO15B	KIAA0408	psi-mi:“MI:0915”(physical association)	0.560
UBASH3A	KIAA0408	psi-mi:“MI:0915”(physical association)	0.560
CCDC57	KIAA0408	psi-mi:“MI:0915”(physical association)	0.560
FRS3	KIAA0408	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (62): SORBS3 (Two-hybrid), KIAA0408 (Two-hybrid), CEP72 (Two-hybrid), KIAA0408 (Two-hybrid), SORBS3 (Two-hybrid), TEX11 (Two-hybrid), KIAA0408 (Two-hybrid), KIAA0408 (Two-hybrid), KIAA0408 (Two-hybrid), KIAA0408 (Two-hybrid), KIAA0408 (Two-hybrid), ABI3 (Two-hybrid), BEGAIN (Two-hybrid), KIAA0408 (Two-hybrid), HOOK2 (Two-hybrid)

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

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 58 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

GO biological processes:

GO term	Partners	Fold	FDR
intermediate filament organization	5	22.3×	2e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	96
Likely benign	9
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1038 predictions. Top by Δscore:

Variant	Effect	Δscore
6:127444110:TAA:T	donor_gain	1.0000
6:127444111:AAA:A	donor_gain	1.0000
6:127449984:A:AC	donor_gain	1.0000
6:127449985:C:CC	donor_gain	1.0000
6:127449985:CTTA:C	donor_gain	1.0000
6:127449988:A:AC	donor_gain	1.0000
6:127449989:C:CC	donor_gain	1.0000
6:127449989:CTGTA:C	donor_gain	1.0000
6:127450348:CAAAG:C	acceptor_gain	1.0000
6:127450349:AAAG:A	acceptor_gain	1.0000
6:127450350:AAG:A	acceptor_gain	1.0000
6:127450350:AAGC:A	acceptor_loss	1.0000
6:127450351:AG:A	acceptor_gain	1.0000
6:127450352:GCT:G	acceptor_loss	1.0000
6:127450353:C:CC	acceptor_gain	1.0000
6:127450353:C:G	acceptor_loss	1.0000
6:127450354:T:A	acceptor_loss	1.0000
6:127444111:AAAC:A	donor_gain	0.9900
6:127449986:TTA:T	donor_loss	0.9900
6:127449987:TA:T	donor_loss	0.9900
6:127449988:ACTG:A	donor_loss	0.9900
6:127449989:C:CA	donor_loss	0.9900
6:127449989:CT:C	donor_gain	0.9900
6:127449989:CTG:C	donor_gain	0.9900
6:127449989:CTGT:C	donor_gain	0.9900
6:127449993:A:AC	donor_gain	0.9900
6:127449994:C:CC	donor_gain	0.9900
6:127450255:A:AC	donor_gain	0.9900
6:127450262:T:A	donor_gain	0.9900
6:127453884:T:A	donor_gain	0.9900

AlphaMissense

4668 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
6:127446985:A:G	F445S	0.988
6:127444201:A:G	W665R	0.987
6:127444201:A:T	W665R	0.987
6:127444199:C:A	W665C	0.986
6:127444199:C:G	W665C	0.986
6:127444244:A:C	F650L	0.984
6:127444244:A:T	F650L	0.984
6:127444246:A:G	F650L	0.984
6:127453888:A:G	W32R	0.984
6:127453888:A:T	W32R	0.984
6:127446984:A:C	F445L	0.983
6:127446984:A:T	F445L	0.983
6:127446986:A:G	F445L	0.983
6:127444216:G:T	R660S	0.981
6:127446969:A:C	F450L	0.980
6:127446969:A:T	F450L	0.980
6:127446971:A:G	F450L	0.980
6:127453886:C:A	W32C	0.980
6:127453886:C:G	W32C	0.980
6:127444202:T:A	R664S	0.977
6:127444202:T:G	R664S	0.977
6:127449875:A:C	S175R	0.974
6:127449875:A:T	S175R	0.974
6:127449877:T:G	S175R	0.974
6:127453907:A:C	F25L	0.974
6:127453907:A:T	F25L	0.974
6:127453909:A:G	F25L	0.974
6:127444203:C:G	R664T	0.972
6:127450351:A:G	L46P	0.967
6:127449867:A:G	L178S	0.964

dbSNP variants (sampled 300 via entrez): RS1000300917 (6:127457735 A>C,G), RS1000364243 (6:127451817 G>A), RS1000703910 (6:127451822 G>A), RS1000754311 (6:127451539 T>A,C), RS1000798788 (6:127451501 C>A), RS1000820181 (6:127442949 A>G), RS1000849952 (6:127456791 G>A,C,T), RS1000907874 (6:127459775 T>C), RS1000959653 (6:127444694 T>A), RS1001152013 (6:127443225 T>C), RS1001215369 (6:127440991 T>A), RS1001256629 (6:127460079 A>G), RS1001403133 (6:127453056 A>C), RS1001524737 (6:127460262 C>A), RS1001772392 (6:127453349 T>C)

Disease associations

OMIM: gene MIM:619236 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

14 associations (top):

Study	Trait	p-value
GCST003254_8	Urinary albumin-to-creatinine ratio in non-diabetics	3.000000e-06
GCST005956_74	Waist-to-hip ratio adjusted for BMI	2.000000e-15
GCST005957_4	Waist-to-hip ratio adjusted for BMI (age <50)	5.000000e-07
GCST005958_6	Waist-to-hip ratio adjusted for BMI (age >50)	2.000000e-11
GCST005962_17	Waist-to-hip ratio adjusted for BMI x sex x age interaction (4df test)	6.000000e-16
GCST007483_20	Waist-to-hip ratio adjusted for BMI (additive genetic model)	7.000000e-19
GCST007487_26	Waist-to-hip ratio adjusted for BMI (additive genetic model)	1.000000e-18
GCST007500_11	Waist-to-hip ratio adjusted for BMI (additive genetic model)	6.000000e-19
GCST007502_26	Waist-to-hip ratio adjusted for BMI (additive genetic model)	5.000000e-19
GCST009798_84	Asthma	3.000000e-10
GCST90020025_529	Waist-to-hip ratio adjusted for BMI	6.000000e-16
GCST90020026_810	Hip index	1.000000e-09
GCST90020027_1049	Waist-hip index	2.000000e-16
GCST90020029_1444	Waist circumference adjusted for body mass index	2.000000e-08

EFO canonical traits (6, from GWAS)

EFO ID	Trait name
EFO:0007778	urinary albumin to creatinine ratio
EFO:0007788	BMI-adjusted waist-hip ratio
EFO:0008007	age at assessment
EFO:0008343	sex interaction measurement
EFO:0008039	BMI-adjusted hip circumference
EFO:0007789	BMI-adjusted waist circumference

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

14 total (human), top 14 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, increases expression	3
Benzo(a)pyrene	affects methylation, decreases expression	2
methylmercuric chloride	increases expression	1
2,5,2’,5’-tetrachlorobiphenyl	decreases expression	1
trichostatin A	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
dorsomorphin	affects cotreatment, increases expression	1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acid	increases expression	1
Estradiol	increases expression, affects cotreatment	1
Silicon Dioxide	decreases expression	1
Tretinoin	increases expression	1
Aflatoxin B1	decreases methylation	1
Okadaic Acid	increases expression	1
Acrylamide	decreases expression	1

Clinical trials (associated diseases)

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