KIAA1549L

Summary

KIAA1549L (KIAA1549 like, HGNC:24836) is a protein-coding gene on chromosome 11p13, encoding UPF0606 protein KIAA1549L (Q6ZVL6).

Predicted to be located in membrane.

Source: NCBI Gene 25758 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 288 total
• MANE Select transcript: NM_012194

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:24836
Approved symbol	KIAA1549L
Name	KIAA1549 like
Location	11p13
Locus type	gene with protein product
Status	Approved
Aliases	G2, MGC34830
Ensembl gene	ENSG00000110427
Ensembl biotype	protein_coding
OMIM	612297
Entrez	25758

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 3 protein_coding

ENST00000265654, ENST00000526400, ENST00000658780

RefSeq mRNA: 2 — MANE Select: NM_012194 NM_001410965, NM_012194

CCDS: CCDS44565, CCDS91457

Canonical transcript exons

ENST00000658780 — 21 exons

Exon	Start	End
ENSE00000710193	33544767	33545378
ENSE00000710208	33559749	33559911
ENSE00000710211	33561676	33561735
ENSE00000710214	33568076	33568227
ENSE00000710216	33574702	33574873
ENSE00000824392	33547764	33547879
ENSE00000824395	33583338	33583501
ENSE00001281991	33667873	33674102
ENSE00001506742	33660863	33661014
ENSE00001506743	33658750	33658898
ENSE00001506745	33656012	33656109
ENSE00001506746	33645686	33646036
ENSE00001506747	33618533	33618662
ENSE00001506749	33609749	33609966
ENSE00001506751	33606641	33606822
ENSE00001506752	33598820	33598947
ENSE00001506754	33591237	33591421
ENSE00001506756	33552108	33552241
ENSE00001506760	33551040	33551259
ENSE00003853303	33541802	33544336
ENSE00003888517	33376108	33376889

Expression profiles

Bgee: expression breadth ubiquitous, 166 present calls, max score 97.25.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 7.3340 / max 445.0339, expressed in 967 samples.

FANTOM5 promoters (10 alternative TSS)

Promoter ID	TPM avg	Samples expressed
113676	4.2778	824
113675	1.3037	564
113679	0.5378	307
113674	0.3738	168
113673	0.1879	88
113680	0.1696	86
113678	0.1584	75
113677	0.1426	63
113681	0.1116	51
113682	0.0708	17

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
middle temporal gyrus	UBERON:0002771	97.25	gold quality
Brodmann (1909) area 23	UBERON:0013554	96.10	gold quality
postcentral gyrus	UBERON:0002581	94.75	gold quality
superior frontal gyrus	UBERON:0002661	94.47	gold quality
endothelial cell	CL:0000115	94.32	gold quality
parietal lobe	UBERON:0001872	94.11	gold quality
entorhinal cortex	UBERON:0002728	92.81	gold quality
cortical plate	UBERON:0005343	90.34	gold quality
primary visual cortex	UBERON:0002436	89.84	gold quality
prefrontal cortex	UBERON:0000451	88.84	gold quality
occipital lobe	UBERON:0002021	88.61	gold quality
frontal cortex	UBERON:0001870	87.97	gold quality
frontal lobe	UBERON:0016525	87.95	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	87.39	gold quality
neocortex	UBERON:0001950	86.90	gold quality
right frontal lobe	UBERON:0002810	85.96	gold quality
cerebral cortex	UBERON:0000956	85.87	gold quality
Brodmann (1909) area 9	UBERON:0013540	85.63	gold quality
secondary oocyte	CL:0000655	85.11	gold quality
ganglionic eminence	UBERON:0004023	83.22	gold quality
telencephalon	UBERON:0001893	82.73	gold quality
cingulate cortex	UBERON:0003027	82.19	gold quality
anterior cingulate cortex	UBERON:0009835	82.03	gold quality
temporal lobe	UBERON:0001871	81.66	gold quality
ventricular zone	UBERON:0003053	81.37	gold quality
right hemisphere of cerebellum	UBERON:0014890	81.09	gold quality
cerebellar cortex	UBERON:0002129	80.97	gold quality
cerebellar hemisphere	UBERON:0002245	80.83	gold quality
cerebellum	UBERON:0002037	80.67	gold quality
cerebellar vermis	UBERON:0004720	80.51	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-HCAD-25	yes	79.01
E-ANND-3	yes	7.39

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

311 targeting KIAA1549L, 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-6867-5P	100.00	82.21	3464
HSA-MIR-4283	100.00	66.42	2097
HSA-MIR-4262	100.00	73.26	3931
HSA-MIR-6833-3P	100.00	70.63	3197
HSA-MIR-4768-5P	100.00	69.49	2861
HSA-MIR-4795-3P	100.00	74.62	4024
HSA-MIR-6873-3P	100.00	71.42	2626
HSA-MIR-126-5P	100.00	72.71	3180
HSA-MIR-7110-3P	100.00	73.18	2486
HSA-MIR-4481	100.00	66.42	1669
HSA-MIR-5193	100.00	67.26	1744
HSA-MIR-656-3P	100.00	72.15	2788
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-29A-3P	100.00	73.11	1835
HSA-MIR-29B-3P	100.00	73.18	1833
HSA-MIR-29C-3P	100.00	73.15	1833
HSA-MIR-5196-5P	100.00	67.98	2761
HSA-MIR-4673	100.00	66.64	1490
HSA-MIR-181A-5P	99.99	72.96	2995
HSA-MIR-181B-5P	99.99	72.97	2996
HSA-MIR-181C-5P	99.99	72.95	2996
HSA-MIR-181D-5P	99.99	73.04	2997
HSA-MIR-33A-5P	99.99	68.62	1055
HSA-MIR-33B-5P	99.99	68.58	1062
HSA-MIR-10401-5P	99.99	65.79	948
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-4745-5P	99.98	65.95	1028
HSA-MIR-4645-5P	99.98	65.81	1284
HSA-MIR-607	99.97	73.62	5593

Literature-anchored findings (GeneRIF, showing 1)

• Four variants in KIAA1549 like (KIAA1549L), a gene previously associated with attempted suicide in bipolar patients, were suggestively associated with being an owl at p < 1.82E-05; post hoc analyses showed the top variant trending in both the Mexican Americans and American Indians cohorts at p = 2.50E-05 and p = .030, respectively (PMID:29192581)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	kiaa1549lb	ENSDARG00000062086
danio_rerio	kiaa1549la	ENSDARG00000062477
mus_musculus	D430041D05Rik	ENSMUSG00000068373
rattus_norvegicus	D430041D05Rikl	ENSRNOG00000011132

Paralogs (1): KIAA1549 (ENSG00000122778)

Protein

Protein identifiers

UPF0606 protein KIAA1549L — Q6ZVL6 (reviewed: Q6ZVL6)

All UniProt accessions (3): A0A590UJI0, A0A5F9UK30, H0YDE5

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Similarity. Belongs to the UPF0606 family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q6ZVL6-1	1	yes
Q6ZVL6-2	2

RefSeq proteins (2): NP_001397894, NP_036326* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR024606	KIAA1549	Family

Pfam: PF12877

UniProt features (22 total): compositionally biased region 8, region of interest 8, splice variant 3, chain 1, transmembrane region 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6ZVL6-F1	44.78	0.05

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 137 (showing top): BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_DN, RIGGI_EWING_SARCOMA_PROGENITOR_UP, TGGAAA_NFAT_Q4_01, MEISSNER_NPC_HCP_WITH_H3K4ME3_AND_H3K27ME3, MIKKELSEN_NPC_HCP_WITH_H3K4ME3_AND_H3K27ME3, CYCLIN_D1_UP.V1_UP, KRAS.300_UP.V1_UP, KRAS.50_UP.V1_UP, KRAS.600_UP.V1_UP, KRAS.600.LUNG.BREAST_UP.V1_UP, KRAS.LUNG_UP.V1_UP, KRAS.LUNG.BREAST_UP.V1_UP, KRAS.PROSTATE_UP.V1_UP, MIR153_5P, MIR6867_5P

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (1): membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	1

Protein interactions and networks

STRING

648 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
KIAA1549L	CSTF3	Q12996	909
KIAA1549L	DEPDC7	Q96QD5	873
KIAA1549L	FBXO3	Q9UK99	872
KIAA1549L	CD59	P13987	650
KIAA1549L	LMO2	P25791	528
KIAA1549L	CSTF1	Q05048	496
KIAA1549L	DPRX	A6NFQ7	467
KIAA1549L	HIPK3	Q9H422	457
KIAA1549L	C11orf91	Q3C1V1	446
KIAA1549L	M9MMK7	M9MMK7	439
KIAA1549L	CT83	Q5H943	396
KIAA1549L	METAP1	P53582	395
KIAA1549L	DNAJC24	Q6P3W2	377
KIAA1549L	CCDC73	Q6ZRK6	377
KIAA1549L	TCP11L1	Q9NUJ3	375

IntAct

6 interactions, top by confidence:

A	B	Type	Score
KIAA1549L	H2BC21	psi-mi:“MI:0915”(physical association)	0.400
KIAA1549L		psi-mi:“MI:0915”(physical association)	0.370
KIAA1549L	FXR1	psi-mi:“MI:0915”(physical association)	0.370
GRB2	KIAA1549L	psi-mi:“MI:0915”(physical association)	0.000
ATXN1	KIAA1549L	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (7): KIAA1549L (Proximity Label-MS), KIAA1549L (Two-hybrid), KIAA1549L (Reconstituted Complex), KIAA1549L (Affinity Capture-MS), KIAA1549L (Affinity Capture-RNA), KIAA1549L (Two-hybrid), KIAA1549L (Two-hybrid)

ESM2 similar proteins: A0A1B0GV85, A1KXC4, A6QLF8, B1ARY8, O14594, O35188, O55145, O60279, O60667, O95196, P07141, P09603, P40225, P40226, P42705, P55066, P55067, P70628, P78423, Q149B8, Q17R60, Q28645, Q2LA85, Q2TB54, Q3TNW5, Q52S86, Q58Y74, Q5IS41, Q5M871, Q5R770, Q5T2D2, Q6PIX9, Q6UXF1, Q6ZVL6, Q7Z434, Q80XH2, Q8BHE4, Q8BT18, Q8C0D9, Q8CAE9

Diamond homologs: Q68FD9, Q6ZVL6, Q9HCM3

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	254
Likely benign	17
Benign	4

Top pathogenic / likely-pathogenic (0)

SpliceAI

3327 predictions. Top by Δscore:

Variant	Effect	Δscore
11:33547762:A:AG	acceptor_gain	1.0000
11:33547763:G:GG	acceptor_gain	1.0000
11:33547763:GTT:G	acceptor_gain	1.0000
11:33547763:GTTCT:G	acceptor_gain	1.0000
11:33547880:G:GG	donor_gain	1.0000
11:33552106:A:AG	acceptor_gain	1.0000
11:33552106:AGT:A	acceptor_gain	1.0000
11:33552107:G:GA	acceptor_gain	1.0000
11:33552107:GT:G	acceptor_gain	1.0000
11:33552107:GTG:G	acceptor_gain	1.0000
11:33552107:GTGCT:G	acceptor_gain	1.0000
11:33552205:G:GT	donor_gain	1.0000
11:33552206:A:T	donor_gain	1.0000
11:33552238:TCAGG:T	donor_loss	1.0000
11:33552239:CAGGT:C	donor_loss	1.0000
11:33552240:AGGTA:A	donor_loss	1.0000
11:33552241:GGTAG:G	donor_loss	1.0000
11:33552243:T:G	donor_loss	1.0000
11:33559736:T:A	acceptor_gain	1.0000
11:33559738:T:TA	acceptor_gain	1.0000
11:33559741:T:A	acceptor_gain	1.0000
11:33559744:TTCAG:T	acceptor_loss	1.0000
11:33559745:TCAGA:T	acceptor_loss	1.0000
11:33559746:CAG:C	acceptor_loss	1.0000
11:33559747:AGA:A	acceptor_loss	1.0000
11:33559748:G:GC	acceptor_gain	1.0000
11:33559748:GA:G	acceptor_gain	1.0000
11:33559907:TGAAC:T	donor_gain	1.0000
11:33559908:GAAC:G	donor_gain	1.0000
11:33559908:GAACG:G	donor_gain	1.0000

AlphaMissense

13813 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
11:33574748:T:C	L1129P	1.000
11:33574786:G:T	G1142W	1.000
11:33583392:C:A	P1189H	1.000
11:33583392:C:G	P1189R	1.000
11:33591249:T:C	F1230L	1.000
11:33591250:T:G	F1230C	1.000
11:33591251:T:A	F1230L	1.000
11:33591251:T:G	F1230L	1.000
11:33609792:G:C	R1405P	1.000
11:33609801:T:C	L1408P	1.000
11:33668081:T:A	L1826H	1.000
11:33668081:T:C	L1826P	1.000
11:33668089:G:C	A1829P	1.000
11:33668093:T:A	I1830N	1.000
11:33668093:T:C	I1830T	1.000
11:33668093:T:G	I1830S	1.000
11:33668096:G:C	R1831P	1.000
11:33668114:T:C	L1837P	1.000
11:33552177:T:C	L967P	0.999
11:33561723:T:A	W1059R	0.999
11:33561723:T:C	W1059R	0.999
11:33561725:G:C	W1059C	0.999
11:33561725:G:T	W1059C	0.999
11:33568148:T:C	L1087P	0.999
11:33574753:T:G	Y1131D	0.999
11:33574756:T:G	Y1132D	0.999
11:33574786:G:A	G1142R	0.999
11:33574786:G:C	G1142R	0.999
11:33574808:T:C	L1149P	0.999
11:33583367:T:A	W1181R	0.999

dbSNP variants (sampled 300 via entrez): RS1000013915 (11:33639186 A>G), RS1000026368 (11:33534985 C>T), RS1000030637 (11:33456473 C>T), RS1000047291 (11:33449882 C>T), RS1000048341 (11:33402744 G>A), RS1000049520 (11:33381433 G>T), RS1000062848 (11:33549187 AT>A), RS1000064645 (11:33418087 T>A), RS1000078956 (11:33402944 T>C), RS1000086675 (11:33528822 G>A), RS1000094279 (11:33593889 T>C,G), RS1000096412 (11:33533766 A>G), RS1000096514 (11:33600547 C>T), RS1000097414 (11:33506560 A>G), RS1000117468 (11:33401688 A>C)

Disease associations

OMIM: gene MIM:612297 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

3 associations (top):

Study	Trait	p-value
GCST001015_2	Suicide attempts in bipolar disorder	4.000000e-06
GCST006585_1604	Blood protein levels	7.000000e-68
GCST009724_76	Vertical cup-disc ratio (multi-trait analysis)	2.000000e-09

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0004321	attempted suicide
EFO:0006939	cup-to-disc ratio measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

48 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression, increases abundance, increases expression	2
belinostat	decreases expression, affects cotreatment	2
Estradiol	affects expression, affects cotreatment, increases expression	2
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
Valproic Acid	decreases expression	2
aristolochic acid I	decreases expression	1
FR900359	increases phosphorylation	1
bisphenol F	decreases expression, affects cotreatment	1
propionaldehyde	increases expression	1
bisphenol A	decreases methylation	1
trichostatin A	increases expression	1
methylparaben	decreases expression	1
benzo(e)pyrene	increases methylation	1
aflatoxin B2	increases methylation	1
2-palmitoylglycerol	increases 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
mirdametinib	affects cotreatment, decreases expression	1
dorsomorphin	decreases expression, affects cotreatment	1
bisphenol S	decreases methylation	1
jinfukang	affects cotreatment, decreases expression	1
(+)-JQ1 compound	affects cotreatment, decreases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Temozolomide	decreases expression	1
Vorinostat	decreases expression	1
Arsenic	decreases expression, increases abundance	1
Atrazine	decreases expression	1
Benzo(a)pyrene	increases methylation	1
Cadmium	decreases expression, increases abundance	1
Cisplatin	affects cotreatment, decreases expression	1

Clinical trials (associated diseases)

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