KIAA1958

Summary

KIAA1958 (HGNC:23427) is a protein-coding gene on chromosome 9q32, encoding Uncharacterized protein KIAA1958 (Q8N8K9).

At a glance

• GWAS associations: 4
• Clinical variants (ClinVar): 52 total
• MANE Select transcript: NM_133465

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:23427
Approved symbol	KIAA1958
Name	KIAA1958
Location	9q32
Locus type	gene with protein product
Status	Approved
Aliases	FLJ39294
Ensembl gene	ENSG00000165185
Ensembl biotype	protein_coding
OMIM	617390
Entrez	158405

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 7 protein_coding

ENST00000337530, ENST00000374244, ENST00000536272, ENST00000866733, ENST00000866734, ENST00000866735, ENST00000951029

RefSeq mRNA: 3 — MANE Select: NM_133465 NM_001287036, NM_001287038, NM_133465

CCDS: CCDS35108, CCDS69642

Canonical transcript exons

ENST00000337530 — 4 exons

Exon	Start	End
ENSE00001091059	112645650	112645822
ENSE00001346022	112659263	112669397
ENSE00001410398	112574057	112575251
ENSE00001892338	112486827	112487118

Expression profiles

Bgee: expression breadth ubiquitous, 200 present calls, max score 90.27.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 8.9667 / max 100.7770, expressed in 1424 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
98053	8.6835	1413
98054	0.1603	75
98055	0.1229	55

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
kidney epithelium	UBERON:0004819	90.27	silver quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	86.87	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	85.62	gold quality
inferior vagus X ganglion	UBERON:0005363	85.30	gold quality
corpus callosum	UBERON:0002336	83.72	gold quality
pigmented layer of retina	UBERON:0001782	83.15	gold quality
renal medulla	UBERON:0000362	82.88	gold quality
dorsal plus ventral thalamus	UBERON:0001897	82.72	silver quality
ventral tegmental area	UBERON:0002691	82.12	silver quality
secondary oocyte	CL:0000655	82.09	gold quality
substantia nigra pars reticulata	UBERON:0001966	82.01	silver quality
subthalamic nucleus	UBERON:0001906	81.95	silver quality
pancreatic ductal cell	CL:0002079	81.70	silver quality
adrenal tissue	UBERON:0018303	81.52	gold quality
ileal mucosa	UBERON:0000331	80.77	gold quality
medulla oblongata	UBERON:0001896	80.64	silver quality
epithelial cell of pancreas	CL:0000083	80.60	gold quality
superior vestibular nucleus	UBERON:0007227	80.31	silver quality
lateral globus pallidus	UBERON:0002476	80.10	silver quality
vena cava	UBERON:0004087	79.66	gold quality
ventricular zone	UBERON:0003053	79.58	gold quality
globus pallidus	UBERON:0001875	79.49	silver quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	79.32	gold quality
body of tongue	UBERON:0011876	78.88	gold quality
endothelial cell	CL:0000115	78.61	silver quality
pons	UBERON:0000988	78.56	silver quality
medial globus pallidus	UBERON:0002477	78.49	silver quality
tongue	UBERON:0001723	78.35	gold quality
islet of Langerhans	UBERON:0000006	78.30	gold quality
Brodmann (1909) area 23	UBERON:0013554	78.15	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

163 targeting KIAA1958, 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-5692A	100.00	74.40	6850
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-3924	100.00	72.09	2394
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-4668-3P	100.00	68.74	2635
HSA-MIR-6867-5P	100.00	82.21	3464
HSA-MIR-3134	100.00	66.43	777
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-4531	99.99	69.70	3181
HSA-MIR-4534	99.99	66.58	1907
HSA-MIR-4500	99.99	72.72	2367
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-8068	99.98	73.85	2376
HSA-MIR-5696	99.98	72.36	4487
HSA-MIR-548P	99.98	72.25	3784
HSA-MIR-1185-1-3P	99.98	71.04	2593
HSA-MIR-1185-2-3P	99.98	71.04	2593
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-3065-5P	99.97	71.56	3281
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-3658	99.96	73.87	4379
HSA-MIR-23A-3P	99.95	74.24	3163
HSA-MIR-23B-3P	99.95	74.24	3163
HSA-MIR-23C	99.95	73.92	3192

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	si:ch211-126i22.5	ENSDARG00000060911
mus_musculus	E130308A19Rik	ENSMUSG00000045071
rattus_norvegicus	Kiaa1958	ENSRNOG00000016780

Paralogs (18): GTF2IRD1 (ENSG00000006704), ZMYM2 (ENSG00000121741), ZMYM5 (ENSG00000132950), THAP12 (ENSG00000137492), ZMYM4 (ENSG00000146463), ZMYM3 (ENSG00000147130), ZMYM6 (ENSG00000163867), GTF2IRD2B (ENSG00000174428), EPM2AIP1 (ENSG00000178567), GTF2IRD2 (ENSG00000196275), ZMYM1 (ENSG00000197056), QRICH1 (ENSG00000198218), FAM200C (ENSG00000221886), FAM200A (ENSG00000221909), SCAND3 (ENSG00000232040), ZBED5 (ENSG00000236287), FAM200B (ENSG00000237765), GTF2I (ENSG00000263001)

Protein

Protein identifiers

Uncharacterized protein KIAA1958 — Q8N8K9 (reviewed: Q8N8K9)

All UniProt accessions (1): Q8N8K9

Isoforms (3)

UniProt ID	Names	Canonical?
Q8N8K9-1	1	yes
Q8N8K9-2	2
Q8N8K9-3	3

RefSeq proteins (3): NP_001273965, NP_001273967, NP_597722* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR021893	ZMYM2-like_C	Domain
IPR042838	KIAA1958	Family

Pfam: PF12012

UniProt features (12 total): cross-link 5, region of interest 2, splice variant 2, chain 1, sequence conflict 1, modified residue 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8N8K9-F1	60.57	0.37

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (6): 97, 201, 204, 237, 283, 626

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 119 (showing top): GTGCCTT_MIR506, NUYTTEN_NIPP1_TARGETS_DN, GEORGES_TARGETS_OF_MIR192_AND_MIR215, KRIEG_HYPOXIA_NOT_VIA_KDM3A, KUMAR_PATHOGEN_LOAD_BY_MACROPHAGES, CAHOY_OLIGODENDROCUTIC, CBX5_TARGET_GENES, GSE13547_2H_VS_12_H_ANTI_IGM_STIM_ZFX_KO_BCELL_UP, LMTK3_TARGET_GENES, RFX7_TARGET_GENES, SNRNP70_TARGET_GENES, ZNF391_TARGET_GENES, ZNF407_TARGET_GENES, ZNF592_TARGET_GENES, ZNF768_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

268 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
KIAA1958	SETD4	Q9NVD3	616
KIAA1958	FTCD	O95954	588
KIAA1958	B4GALT6	Q9UBX8	587
KIAA1958	TTC38	Q5R3I4	547
KIAA1958	TTC34	A8MYJ7	536
KIAA1958	TRPM3	Q9HCF6	444
KIAA1958	ZNF76	P36508	433
KIAA1958	ZNF785	A8K8V0	425
KIAA1958	ZNF606	Q8WXB4	424
KIAA1958	ENOSF1	Q7L5Y1	423
KIAA1958	ZNF708	P17019	420
KIAA1958	ZNF385B	Q569K4	414
KIAA1958	ZNF256	Q9Y2P7	407
KIAA1958	CIZ1	Q9ULV3	406
KIAA1958	RCAN3	Q9UKA8	388

IntAct

61 interactions, top by confidence:

A	B	Type	Score
KIAA1958	GABARAPL2	psi-mi:“MI:0915”(physical association)	0.780
GABARAPL2	KIAA1958	psi-mi:“MI:0915”(physical association)	0.780
SOCS3	KIAA1958	psi-mi:“MI:0915”(physical association)	0.720
KIAA1958	LMO4	psi-mi:“MI:0915”(physical association)	0.720
TCEA2	KIAA1958	psi-mi:“MI:0915”(physical association)	0.720
LMO4	KIAA1958	psi-mi:“MI:0915”(physical association)	0.720
KIAA1958	TCEA2	psi-mi:“MI:0915”(physical association)	0.720
AQP1	KIAA1958	psi-mi:“MI:0915”(physical association)	0.560
KIAA1958	RWDD2B	psi-mi:“MI:0915”(physical association)	0.560
COASY	KIAA1958	psi-mi:“MI:0915”(physical association)	0.560
STAC	KIAA1958	psi-mi:“MI:0915”(physical association)	0.560
MCRS1	KIAA1958	psi-mi:“MI:0915”(physical association)	0.560
KIAA1958	CEP19	psi-mi:“MI:0915”(physical association)	0.560
KIAA1958	FAM124B	psi-mi:“MI:0915”(physical association)	0.560
KIAA1958	AQP1	psi-mi:“MI:0915”(physical association)	0.560
KIAA1958	MCRS1	psi-mi:“MI:0915”(physical association)	0.560
CEP19	KIAA1958	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (28): KIAA1958 (Two-hybrid), KIAA1958 (Two-hybrid), KIAA1958 (Two-hybrid), KIAA1958 (Two-hybrid), KIAA1958 (Two-hybrid), KIAA1958 (Two-hybrid), KIAA1958 (Two-hybrid), KIAA1958 (Two-hybrid), KIAA1958 (Two-hybrid), KIAA1958 (Two-hybrid), KIAA1958 (Two-hybrid), KIAA1958 (Two-hybrid), KIAA1958 (Affinity Capture-MS), KIAA1958 (Affinity Capture-MS), KIAA1958 (Affinity Capture-RNA)

ESM2 similar proteins: A3KMX0, A4IFA3, A4IGY9, A4Z943, A4Z944, B8QB46, D2EAC2, E1C2V1, O43422, O60290, P10911, P35125, P86452, Q13075, Q2NKX8, Q3UPF5, Q49AG3, Q5FWF4, Q5SVZ6, Q5T890, Q5TKR9, Q6DJS0, Q6EKJ0, Q6R2W3, Q6YI93, Q7Z2W4, Q80WE4, Q86UP8, Q86VD1, Q8BZ21, Q8N8K9, Q8QMP8, Q8TDB6, Q8WML3, Q92794, Q96JM7, Q96JS3, Q99388, Q99NI3, Q9CUX1

Diamond homologs: Q8C4P0, Q8N8K9

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	44
Likely benign	4
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1515 predictions. Top by Δscore:

Variant	Effect	Δscore
9:112617859:A:AG	acceptor_gain	1.0000
9:112617859:AATTT:A	acceptor_gain	1.0000
9:112617860:A:AG	acceptor_gain	1.0000
9:112617861:T:G	acceptor_gain	1.0000
9:112617863:T:A	acceptor_gain	1.0000
9:112617867:GCA:G	acceptor_loss	1.0000
9:112617869:A:AG	acceptor_gain	1.0000
9:112617870:G:GA	acceptor_gain	1.0000
9:112617870:GACC:G	acceptor_gain	1.0000
9:112617870:GACCA:G	acceptor_gain	1.0000
9:112487116:CAG:C	donor_loss	0.9900
9:112487117:AG:A	donor_loss	0.9900
9:112487119:GTGG:G	donor_gain	0.9900
9:112490199:T:G	donor_gain	0.9900
9:112490199:T:TG	donor_gain	0.9900
9:112617860:ATTT:A	acceptor_gain	0.9900
9:112617866:T:A	acceptor_gain	0.9900
9:112617870:GA:G	acceptor_gain	0.9900
9:112617870:GAC:G	acceptor_gain	0.9900
9:112490164:GAT:G	donor_gain	0.9800
9:112490186:G:GT	donor_gain	0.9800
9:112545301:T:G	donor_gain	0.9800
9:112487115:GCAG:G	donor_gain	0.9600
9:112490166:T:G	donor_gain	0.9600
9:112555693:GACC:G	donor_gain	0.9600
9:112602522:G:GT	donor_gain	0.9600
9:112487117:AGGTG:A	donor_gain	0.9500
9:112490160:ACC:A	donor_gain	0.9500
9:112574056:GGA:G	acceptor_gain	0.9500
9:112487116:CAGGT:C	donor_gain	0.9400

AlphaMissense

4733 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
9:112574124:T:C	L15S	1.000
9:112574124:T:G	L15W	1.000
9:112574127:T:A	V16D	1.000
9:112574132:T:A	W18R	1.000
9:112574132:T:C	W18R	1.000
9:112574133:G:C	W18S	1.000
9:112574134:G:C	W18C	1.000
9:112574134:G:T	W18C	1.000
9:112574135:G:C	A19P	1.000
9:112574136:C:A	A19D	1.000
9:112574138:C:G	H20D	1.000
9:112574144:C:G	H22D	1.000
9:112574147:G:T	G23W	1.000
9:112574156:T:C	C26R	1.000
9:112574157:G:A	C26Y	1.000
9:112574158:C:G	C26W	1.000
9:112574169:C:A	P30Q	1.000
9:112574222:T:A	W48R	1.000
9:112574222:T:C	W48R	1.000
9:112574223:G:C	W48S	1.000
9:112574224:G:C	W48C	1.000
9:112574224:G:T	W48C	1.000
9:112574228:T:A	C50S	1.000
9:112574228:T:C	C50R	1.000
9:112574229:G:A	C50Y	1.000
9:112574229:G:C	C50S	1.000
9:112574230:T:G	C50W	1.000
9:112574240:C:G	H54D	1.000
9:112574242:T:A	H54Q	1.000
9:112574242:T:G	H54Q	1.000

dbSNP variants (sampled 300 via entrez): RS1000012735 (9:112522986 G>A), RS1000040225 (9:112556695 T>C), RS1000044836 (9:112637713 A>G), RS1000092182 (9:112556468 T>C), RS1000114037 (9:112653673 G>A), RS1000133533 (9:112511937 A>G), RS1000159975 (9:112622186 A>G), RS1000189979 (9:112609272 T>A,C), RS1000191889 (9:112520596 A>G), RS1000212273 (9:112625158 C>T), RS1000221060 (9:112608907 T>C), RS1000233371 (9:112562787 T>C), RS1000249369 (9:112569345 T>C), RS1000278807 (9:112492074 T>G), RS1000282734 (9:112550213 A>C,T)

Disease associations

OMIM: gene MIM:617390 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

4 associations (top):

Study	Trait	p-value
GCST002930_13	Cobalt levels	6.000000e-06
GCST004402_4	Reading disability or specific language impairment adjusted for intelligence quotient (pleiotropy)	1.000000e-06
GCST007508_1	Self-reported childhood asthma in adult smokers	5.000000e-08
GCST009257_5	Caudate nucleus volume	1.000000e-06

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0004337	intelligence
EFO:0004830	caudate nucleus volume

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

22 total (human), top 22 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, decreases expression	7
trichostatin A	affects cotreatment, decreases expression	3
aristolochic acid I	decreases expression	1
FR900359	increases phosphorylation	1
sodium arsenite	decreases expression, increases abundance	1
perfluorooctane sulfonic acid	decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
abrine	decreases expression	1
2,2’,4,4’-tetrabromodiphenyl ether	increases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
(+)-JQ1 compound	increases expression	1
Vorinostat	decreases expression	1
Arsenic	decreases expression, increases abundance	1
Atrazine	increases expression	1
Benzo(a)pyrene	decreases methylation	1
Cisplatin	decreases expression	1
Doxorubicin	decreases expression	1
Sodium Dodecyl Sulfate	increases expression	1
Tretinoin	decreases expression	1
Urethane	increases expression	1
Vanadates	decreases expression	1
Lactic Acid	decreases expression	1

Clinical trials (associated diseases)

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