SCAND3

Summary

SCAND3 (SCAN domain containing 3, HGNC:13851) is a protein-coding gene on chromosome 6p22.1, encoding SCAN domain-containing protein 3 (Q6R2W3).

Predicted to enable nucleic acid binding activity. Involved in positive regulation of cell cycle and positive regulation of epithelial cell proliferation. Located in cytoplasm.

Source: NCBI Gene 114821 — automated summary from GO annotations (Alliance of Genome Resources).

At a glance

• GWAS associations: 30 (top 4% of genes corpus-wide)
• Clinical variants (ClinVar): 84 total
• GTEx eGene: eQTL in 13 tissues, sQTL in 1 (q < 0.05)
• Constraint (gnomAD): pLI 0.00 (LoF-tolerant), LOEUF 0.59 (moderately constrained)
• MANE Select transcript: NM_052923
• Notable: 84 clinical variants but no curated precision-oncology (CIViC) evidence yet

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:13851
Approved symbol	SCAND3
Name	SCAN domain containing 3
Location	6p22.1
Locus type	gene with protein product
Status	Approved
Aliases	ZFP38-L, KIAA1925, FLJ31087, Buster4, FAM200D
Ensembl gene	ENSG00000232040
Ensembl biotype	protein_coding
OMIM	615254
Entrez	114821

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 4 protein_coding, 3 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

MANE Select: ENST00000452236

Transcript support level (Ensembl TSL; 1 = fully mRNA-supported): TSL 1: 1, TSL 2: 1, TSL 3: 1, TSL 4: 1

ENST00000452236, ENST00000524745, ENST00000526291, ENST00000530247, ENST00000646382, ENST00000927696, ENST00000983442, ENST00001141618

RefSeq mRNA: 2 — MANE Select: NM_052923 NM_001329616, NM_052923

CCDS: CCDS34355, CCDS87376

Canonical transcript exons

ENST00000452236 — 4 exons

Exon	Start	End
ENSE00002439661	28574644	28576136
ENSE00002480261	28586298	28587298
ENSE00003522808	28579272	28579419
ENSE00003821209	28570535	28573827

Expression profiles

Bgee: expression breadth ubiquitous, 170 present calls, max score 81.69.

FANTOM5 (CAGE): breadth broad, TPM avg 2.1797 / max 34.4213, expressed in 783 samples.

Highest expression (Bgee): primordial germ cell in gonad, testis, secondary oocyte, male germ line stem cell (sensu Vertebrata) in testis, ganglionic eminence.

Genetic regulation across tissues (GTEx eQTL / sQTL)

SCAND3 is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 13 tissues and its splicing (sQTL) in 1 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.

14 significant tissue × QTL associations:

Tissue	QTL	q-value	Slope	Lead variant
Testis	eqtl	1.4e-13	+0.29	6:28557488:A:G
Artery Aorta	eqtl	2.3e-07	-0.35	6:28803421:T:C
Artery Tibial	eqtl	2.4e-06	-0.23	6:28554918:A:G
Pancreas	eqtl	5.4e-04	-0.36	6:27820212:G:A
Nerve Tibial	eqtl	1.3e-03	+0.24	6:29431161:T:C
Colon Transverse	eqtl	5.4e-03	-0.51	6:28347433:C:T
Esophagus Muscularis	eqtl	1.6e-02	+0.17	6:28674180:A:G
Thyroid	eqtl	1.8e-02	+0.19	6:28905384:A:C
Esophagus Mucosa	eqtl	1.8e-02	-0.16	6:28689413:G:A
Skin Not Sun Exposed Suprapubic	eqtl	2.2e-02	-0.29	6:27691828:G:T
Testis	sqtl	2.6e-02	-0.36	6:27891059:T:C
Adipose Subcutaneous	eqtl	2.8e-02	-0.28	6:28194273:C:G
Brain Hippocampus	eqtl	2.9e-02	+0.26	6:29565804:AATAG:A
Minor Salivary Gland	eqtl	3.3e-02	+0.49	6:28826496:G:C

FANTOM5 promoters

6 alternative TSS:

Promoter ID	TPM avg	Samples expressed
72426	1.8098	730
72429	0.1276	42
72428	0.0868	35
72427	0.0761	35
72425	0.0568	21
72430	0.0226	14

Top tissues by expression

showing 100 of 250 tissues by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	81.69	gold quality
left testis	UBERON:0004533	80.00	gold quality
testis	UBERON:0000473	79.93	gold quality
right testis	UBERON:0004534	79.39	gold quality
secondary oocyte	CL:0000655	79.28	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	77.54	gold quality
ganglionic eminence	UBERON:0004023	75.98	gold quality
corpus epididymis	UBERON:0004359	74.96	gold quality
cortical plate	UBERON:0005343	74.86	gold quality
ventricular zone	UBERON:0003053	73.92	gold quality
adrenal tissue	UBERON:0018303	73.48	gold quality
oocyte	CL:0000023	73.05	gold quality
islet of Langerhans	UBERON:0000006	70.75	gold quality
sperm	CL:0000019	70.42	gold quality
sural nerve	UBERON:0015488	70.32	gold quality
cerebellar hemisphere	UBERON:0002245	67.67	gold quality
cerebellar cortex	UBERON:0002129	67.56	gold quality
cerebellum	UBERON:0002037	66.99	gold quality
right hemisphere of cerebellum	UBERON:0014890	66.90	gold quality
seminal vesicle	UBERON:0000998	65.56	gold quality
caput epididymis	UBERON:0004358	64.22	gold quality
prefrontal cortex	UBERON:0000451	63.97	gold quality
rectum	UBERON:0001052	62.85	gold quality
pancreas	UBERON:0001264	62.75	gold quality
tibialis anterior	UBERON:0001385	61.86	silver quality
right lobe of liver	UBERON:0001114	61.79	gold quality
ileal mucosa	UBERON:0000331	61.43	silver quality
pigmented layer of retina	UBERON:0001782	61.29	gold quality
right adrenal gland cortex	UBERON:0035827	60.63	gold quality
right adrenal gland	UBERON:0001233	60.59	gold quality
stromal cell of endometrium	CL:0002255	60.45	gold quality
metanephros	UBERON:0000081	60.35	gold quality
body of pancreas	UBERON:0001150	60.23	gold quality
oviduct epithelium	UBERON:0004804	59.81	silver quality
pituitary gland	UBERON:0000007	59.80	gold quality
frontal cortex	UBERON:0001870	59.41	gold quality
Brodmann (1909) area 9	UBERON:0013540	59.28	gold quality
adenohypophysis	UBERON:0002196	59.27	gold quality
placenta	UBERON:0001987	59.18	gold quality
right lobe of thyroid gland	UBERON:0001119	59.16	gold quality
prostate gland	UBERON:0002367	59.14	gold quality
left lobe of thyroid gland	UBERON:0001120	58.95	gold quality
ovary	UBERON:0000992	58.79	gold quality
neocortex	UBERON:0001950	58.77	gold quality
thyroid gland	UBERON:0002046	58.75	gold quality
left adrenal gland	UBERON:0001234	58.70	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	58.59	gold quality
right frontal lobe	UBERON:0002810	58.58	gold quality
adult organism	UBERON:0007023	58.58	gold quality
fallopian tube	UBERON:0003889	58.48	gold quality
cauda epididymis	UBERON:0004360	58.48	gold quality
endothelial cell	CL:0000115	58.42	gold quality
adrenal gland	UBERON:0002369	58.42	gold quality
left ovary	UBERON:0002119	58.04	gold quality
liver	UBERON:0002107	57.39	gold quality
right uterine tube	UBERON:0001302	57.28	gold quality
pancreatic ductal cell	CL:0002079	57.22	silver quality
left adrenal gland cortex	UBERON:0035825	57.17	gold quality
nucleus accumbens	UBERON:0001882	56.89	gold quality
adrenal cortex	UBERON:0001235	56.66	gold quality
right ovary	UBERON:0002118	56.42	gold quality
metanephros cortex	UBERON:0010533	56.30	gold quality
body of uterus	UBERON:0009853	56.27	gold quality
hypothalamus	UBERON:0001898	56.18	gold quality
cerebral cortex	UBERON:0000956	55.99	gold quality
brain	UBERON:0000955	55.96	gold quality
smooth muscle tissue	UBERON:0001135	55.90	gold quality
cortex of kidney	UBERON:0001225	55.84	gold quality
anterior cingulate cortex	UBERON:0009835	55.50	gold quality
adult mammalian kidney	UBERON:0000082	55.26	gold quality
forebrain	UBERON:0001890	54.95	gold quality
kidney	UBERON:0002113	54.86	gold quality
endocervix	UBERON:0000458	54.63	gold quality
endometrium	UBERON:0001295	54.50	gold quality
cardiac muscle of right atrium	UBERON:0003379	54.34	gold quality
ectocervix	UBERON:0012249	54.34	gold quality
epithelial cell of pancreas	CL:0000083	54.31	gold quality
left ventricle myocardium	UBERON:0006566	54.23	gold quality
female reproductive system	UBERON:0000474	54.20	gold quality
tibia	UBERON:0000979	54.12	silver quality
caudate nucleus	UBERON:0001873	54.09	gold quality
kidney epithelium	UBERON:0004819	53.93	gold quality
deltoid	UBERON:0001476	53.58	gold quality
left uterine tube	UBERON:0001303	53.56	gold quality
upper arm skin	UBERON:0004263	53.52	gold quality
bronchial epithelial cell	CL:0002328	53.50	silver quality
colonic epithelium	UBERON:0000397	53.46	gold quality
uterine cervix	UBERON:0000002	53.43	gold quality
uterus	UBERON:0000995	53.38	gold quality
bronchus	UBERON:0002185	52.88	silver quality
gall bladder	UBERON:0002110	52.72	gold quality
vermiform appendix	UBERON:0001154	52.40	gold quality
minor salivary gland	UBERON:0001830	51.97	gold quality
bone marrow cell	CL:0002092	51.90	gold quality
heart left ventricle	UBERON:0002084	51.79	gold quality
cardiac ventricle	UBERON:0002082	51.39	gold quality
saliva-secreting gland	UBERON:0001044	51.25	gold quality
heart	UBERON:0000948	51.16	gold quality
putamen	UBERON:0001874	50.62	gold quality
lymph node	UBERON:0000029	50.61	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.34

HPA expression

RNA tissue specificity: Tissue enhanced

showing 60 of 73 HPA tissues / cells by nTPM:

Tissue / cell	Axis	nTPM
Testis	tissue	8.1
Caudate putamen	tissue	5.1
Frontal cortex	tissue	4.4
Postcentral gyrus	tissue	3.4
Epididymis	tissue	2.9
Cerebellum	tissue	2.7
Locus coeruleus	tissue	2.5
Hippocampal formation	tissue	2.4
Nucleus accumbens	tissue	2.3
Olfactory bulb	tissue	2.3
Hypothalamus	tissue	2.2
Hippocampus	tissue	2.1
Periaqueductal gray	tissue	2.1
Midbrain	tissue	1.9
Thalamus	tissue	1.9
Septum	tissue	1.9
Cerebral cortex	tissue	1.8
Pons	tissue	1.8
Motor cortex	tissue	1.8
Prefrontal cortex	tissue	1.7
Seminal vesicle	tissue	1.7
Basal ganglia	tissue	1.7
Amygdala	tissue	1.7
Entorhinal cortex	tissue	1.7
Putamen	tissue	1.6
Choroid plexus	tissue	1.6
Substantia nigra	tissue	1.6
Thyroid gland	tissue	1.6
Spinal cord	tissue	1.6
Corpus callosum	tissue	1.6
Ventral forebrain	tissue	1.6
Retrosplenial cortex	tissue	1.6
Temporal cortex	tissue	1.6
Medulla oblongata	tissue	1.5
Superior colliculi	tissue	1.5
Retrosplenial and cingulate cortex	tissue	1.5
Somatosensory cortex	tissue	1.5
Occipital cortex	tissue	1.5
Insular cortex	tissue	1.5
Retina	tissue	1.4
Prostate	tissue	1.3
Ovary	tissue	1.1
Liver	tissue	1.1
Fallopian tube	tissue	1.1
Parathyroid gland	tissue	0.9
Cervix	tissue	0.8
Breast	tissue	0.8
Kidney	tissue	0.8
Salivary gland	tissue	0.7
Placenta	tissue	0.6
Pituitary gland	tissue	0.5
Rectum	tissue	0.5
Endometrium 1	tissue	0.5
Pancreas	tissue	0.4
Lung	tissue	0.4
Adrenal gland	tissue	0.4
Thymus	tissue	0.4
Stomach 1	tissue	0.3
Smooth muscle	tissue	0.3
Colon	tissue	0.3

Brain sub-regions (HPA Brain Atlas): detected in 189; highest nTPM — Cerebellar cortex (5.0), Flocculonodular lobe (4.6), Vermis (4.6), Stria terminalis, bed nucleus (3.4), Transversal temporal gyrus, anterior (3.2).

Regulation

Is transcription factor: yes

JASPAR motifs

Motif	Name	Family
MA2542.1	SCAND3	BED zinc finger factors

JASPAR matrix evidence (PMIDs): PMID:39605530

miRNA regulators (miRDB)

Targeting SCAND3 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific).

15 miRNAs:

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-MIR-4307	99.82	70.45	3374
HSA-MIR-3121-3P	99.82	71.96	3630
HSA-MIR-33A-3P	99.70	70.27	3362
HSA-MIR-561-3P	99.64	70.90	3647
HSA-MIR-3609	99.52	69.89	2587
HSA-MIR-548AH-5P	99.52	69.73	2626
HSA-MIR-3915	99.45	68.49	1905
HSA-MIR-421	98.90	67.04	1883
HSA-MIR-1-5P	98.70	68.66	1017
HSA-MIR-4305	97.94	68.63	533
HSA-MIR-1295B-3P	96.68	66.11	276
HSA-MIR-4524B-3P	95.52	64.12	964

Functional genomics

gnomAD constraint: pLI 9.16e-05, LOEUF 0.592, missense Z 3.61 — population loss-of-function intolerance (pLI ≥ 0.9 = LoF-intolerant; lower LOEUF = more constrained). gnomAD

Regional missense constraint (gnomAD RMC): no regional variation along ENST00000452236 — one region, missense o/e 0.80.

Literature-anchored findings (GeneRIF, showing 3)

• the present study indicated that ZNF452 may be an upstream regulator of AKT-GSK3beta signaling pathway and facilitates proliferation and invasion of non-small cell lung cancer (PMID:28418919)
• Genome-wide association study on blood pressure traits in the Iranian population suggests ZBED9 as a new locus for hypertension. (PMID:34083597)
• The AGT epistasis pattern proposed a novel role for ZBED9 in regulating blood pressure: Tehran Cardiometabolic genetic study (TCGS). (PMID:35577038)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Zbed5	ENSMUSG00000034173
rattus_norvegicus	Zbed5	ENSRNOG00000000918

Paralogs (18): GTF2IRD1 (ENSG00000006704), ZMYM2 (ENSG00000121741), ZMYM5 (ENSG00000132950), THAP12 (ENSG00000137492), ZMYM4 (ENSG00000146463), ZMYM3 (ENSG00000147130), ZMYM6 (ENSG00000163867), KIAA1958 (ENSG00000165185), GTF2IRD2B (ENSG00000174428), EPM2AIP1 (ENSG00000178567), GTF2IRD2 (ENSG00000196275), ZMYM1 (ENSG00000197056), QRICH1 (ENSG00000198218), FAM200C (ENSG00000221886), FAM200A (ENSG00000221909), ZBED5 (ENSG00000236287), FAM200B (ENSG00000237765), GTF2I (ENSG00000263001)

Additional cross-species homologs

Sequence homologs in species beyond Ensembl Compara’s model organisms, by Diamond local protein alignment (% sequence identity; best hit per species). Lower-identity rows are more distant homologs. The matched accessions’ gene symbols aren’t in biobtree yet, so each row shows the UniProt accession.

Organism	UniProt	Identity	Method
Gorilla gorilla gorilla	A1YEW3	100.0%	Diamond
Pan paniscus	A1YG26	100.0%	Diamond
Pan troglodytes	A2T715	100.0%	Diamond
Pongo abelii	Q5RAE6	100.0%	Diamond
Pongo pygmaeus	A2T812	98.7%	Diamond
Macaca nemestrina	A2T6E3	98.3%	Diamond
Canis lupus familiaris	A4Z944	98.3%	Diamond
Bos taurus	A4Z943	97.4%	Diamond
Macaca fascicularis	Q4R6P1	96.5%	Diamond

Genomic neighbors (locus context)

Genes flanking this one on the chromosome (NCBI/Entrez gene neighborhood). Positional context only — some neighbors share regulatory elements (bidirectional promoters, antisense/overlapping transcripts), but chromosomal adjacency is not itself a functional relationship (see Interactions for that).

Symbol	Type	Entrez
TRQ-TTG2-1	tRNA	100189138
TRS-GCT4-1	tRNA	100189225
TRI-TAT3-1	tRNA	100189348
ZBED9-AS1	ncRNA	121676925
GPX5	protein-coding	2880
TRR-TCG5-1	tRNA	100189034
TRA-AGC3-1	tRNA	100189299
GPX6	protein-coding	257202
TRA-TGC2-1	tRNA	100189114
TRT-CGT3-1	tRNA	100189360

Protein

Protein identifiers

SCAN domain-containing protein 3 — Q6R2W3 (reviewed: Q6R2W3)

Alternative names: Transposon-derived Buster4 transposase-like protein, Zinc finger BED domain-containing protein 9

All UniProt accessions (3): A0A1U9X8W9, A0A2R8Y5N3, Q6R2W3

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Nucleus.

Tissue specificity. Weakly expressed in the lung (at protein level).

Miscellaneous. Highly expressed in non-small-cell lung carcinoma (NSCLC) tissue, with increased expression correlating with advanced disease, lymph node metastases and poor prognosis, as such may be a candidate prognostic marker. May act as an oncogene and promote tumor growth via positive regulation of cell cycle progression at G1/S phase transition. May promote invasion and metastasis via activation of the AKT/GSK-3 beta signaling pathway. Expressed in the cytoplasm in NSCLC tissue. May be derived from an ancient transposon that has lost its ability to translocate.

RefSeq proteins (2): NP_001316545, NP_443155* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001584	Integrase_cat-core	Domain
IPR003309	SCAN_dom	Domain
IPR012337	RNaseH-like_sf	Homologous_superfamily
IPR036397	RNaseH_sf	Homologous_superfamily
IPR038269	SCAN_sf	Homologous_superfamily
IPR057560	Znf_SCAND3	Domain

Pfam: PF02023, PF23663, PF27046, PF27073

UniProt features (13 total): sequence conflict 6, domain 2, coiled-coil region 2, sequence variant 2, chain 1

Structure

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6R2W3-F1	72.39	0.28

Human Protein Atlas

Protein class: Predicted intracellular proteins

Protein evidence: Evidence at protein level

Subcellular location (HPA, imaging): nucleoli; golgi apparatus; nucleoplasm

Antibody reliability (HPA): IH uncertain · IF approved

Function

Pathways and Gene Ontology

Reactome pathways

0 curated (TAS) of 0; 0 disease pathways. Curated-first; evidence = TAS (manually curated) vs IEA (electronic inference).

MSigDB gene sets: 55 (showing top): RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_UP, GOBP_DNA_INTEGRATION, ACEVEDO_LIVER_CANCER_WITH_H3K27ME3_UP, MODULE_205, KOYAMA_SEMA3B_TARGETS_UP, GOBP_REGULATION_OF_CELL_CYCLE, GOBP_EPITHELIAL_CELL_PROLIFERATION, GOBP_POSITIVE_REGULATION_OF_CELL_CYCLE, GOBP_DNA_METABOLIC_PROCESS, GOBP_POSITIVE_REGULATION_OF_CELL_POPULATION_PROLIFERATION, HMG20B_TARGET_GENES, HOXA7_TARGET_GENES, KLF14_TARGET_GENES, PGBD5_TARGET_GENES, SKIL_TARGET_GENES

GO Biological Process (3): DNA integration (GO:0015074), positive regulation of cell cycle (GO:0045787), positive regulation of epithelial cell proliferation (GO:0050679)

GO Molecular Function (2): nucleic acid binding (GO:0003676), protein dimerization activity (GO:0046983)

GO Cellular Component (2): nucleus (GO:0005634), cytoplasm (GO:0005737)

GO top-level categories

12 GO namespaces:

Category	Terms
DNA metabolic process	1
cell cycle	1
positive regulation of cellular process	1
regulation of cell cycle	1
positive regulation of cell population proliferation	1
epithelial cell proliferation	1
regulation of epithelial cell proliferation	1
binding	1
protein binding	1
intracellular membrane-bounded organelle	1
intracellular anatomical structure	1
cellular anatomical structure	1

Experimentally-supported GO annotations

GO terms backed by direct experimental evidence (ECO experimental codes) — 3 of 7 annotations. The rest are phylogenetic / computational / electronic (IEA).

3 experimentally-supported GO terms:

GO term	NS	Evidence
positive regulation of cell cycle	BP	mutant phenotype
positive regulation of epithelial cell proliferation	BP	mutant phenotype
cytoplasm	CC	direct assay

Protein interactions and networks

STRING

showing 15 of 494 interactions by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SCAND3	TSGA10IP	Q3SY00	548
SCAND3	XKR5	Q6UX68	536
SCAND3	SPDYE5	A6NIY4	430
SCAND3	ZBED4	O75132	426
SCAND3	DMBX1	Q8NFW5	381
SCAND3	TRIM69	Q86WT6	370
SCAND3	ANGPTL7	O43827	366
SCAND3	EXOC3L4	Q17RC7	365
SCAND3	SGIP1	Q9BQI5	357
SCAND3	ZNF280A	P59817	350
SCAND3	ZBED1	O96006	345
SCAND3	GIN1	Q9NXP7	345
SCAND3	GPR31	O00270	344
SCAND3	SLC5A9	Q2M3M2	341
SCAND3	VSIG8	P0DPA2	340

IntAct

Human interaction partners of SCAND3 in IntAct, one row per partner (best MIscore; records = supporting IntAct interaction records).

2 partners by confidence:

Partner	Interaction type	MIscore	Records
KPNA4	physical association	0.400	1
KRBA2	physical association	0.400	1

Disease & clinical

Genetic variants

Variant evidence for SCAND3: 84 ClinVar records (0 pathogenic / likely pathogenic); 30 GWAS associations.

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	75
Likely benign	3
Benign	0

SpliceAI

Top 10 splice-impact sites by Δscore (adjacent positions with the same effect merged into one range; 28 predictions of 203):

Position(s)	Effect	Δscore	Sites
6:28579420–28579421	acceptor_loss	1.0000	6
6:28579270–28579271	donor_loss	0.9900	6
6:28579277	donor_gain	0.9900
6:28586296–28586297	donor_loss	0.9900	5
6:28573828–28573829	acceptor_loss	0.9800	4
6:28573834	acceptor_gain	0.9800
6:28579422	acceptor_loss	0.9800
6:28586296	donor_loss	0.9800
6:28573828–28573829	acceptor_loss	0.9700	2
6:28581859	donor_gain	0.9700

AlphaMissense

1,931 missense substitutions predicted likely pathogenic (of 8,798 scored), across 556 residues. Top 20 hotspot residues, ranked by the number of likely-pathogenic substitutions (of those reachable by a single-nucleotide change), then by mean score:

Residue	Likely-pathogenic substitutions	Mean am_pathogenicity	Max am_pathogenicity
M326	9	0.888	0.970
H315	8	0.942	0.982
F746	8	0.933	0.995
F308	8	0.929	0.994
H779	8	0.895	0.972
F244	8	0.883	0.982
N336	8	0.868	0.973
H320	8	0.864	0.959
H784	8	0.861	0.953
H1325	8	0.816	0.927
D423	8	0.790	0.896
F276	7	0.965	0.994
C349	7	0.963	0.981
F226	7	0.955	0.992
C762	7	0.941	0.982
C352	7	0.940	0.963
C852	7	0.939	0.996
W80	7	0.934	0.982
F795	7	0.934	0.972
E841	7	0.934	0.982

HPA cancer prognostics

RNA cancer specificity: Low cancer specificity

Human Protein Atlas survival analysis — favorable = higher expression predicts better survival.

1 prognostic cancer types:

Cancer	Prognostic	p-value
Kidney Renal Clear Cell Carcinoma (TCGA)	favorable	0.000124

Disease associations

OMIM: gene MIM:615254 | disease phenotypes:

GWAS associations

30 associations:

Study	Trait	p-value
GCST90016674_3	Liver iron content	1e-89
GCST004521_212	Autism spectrum disorder or schizophrenia	2e-27
GCST004521_263	Autism spectrum disorder or schizophrenia	3e-26
GCST010241_27	Apolipoprotein A1 levels	9e-25
GCST004521_117	Autism spectrum disorder or schizophrenia	4e-24
GCST004521_216	Autism spectrum disorder or schizophrenia	1e-19
GCST010083_324	Hemoglobin levels	1e-17
GCST010703_224	Brain morphology (MOSTest)	7e-16
GCST004521_158	Autism spectrum disorder or schizophrenia	2e-15
GCST004521_88	Autism spectrum disorder or schizophrenia	5e-14
GCST007326_87	Number of sexual partners	2e-13
GCST010988_324	Adult body size	2e-13
GCST004748_95	Lung cancer	1e-12
GCST012355_12	Depression	2e-12
GCST90020028_680	Hip circumference adjusted for BMI	2e-12
GCST010142_7	Fish- and plant-related diet	3e-12
GCST004750_18	Squamous cell lung carcinoma	1e-11
GCST008921_4	Asthma and major depressive disorder	2e-11
GCST010702_125	Subcortical volume (MOSTest)	3e-11
GCST004521_7	Autism spectrum disorder or schizophrenia	8e-11
GCST010142_16	Fish- and plant-related diet	2e-10
GCST006291_39	Spherical equivalent or myopia (age of diagnosis)	3e-10
GCST010142_19	Fish- and plant-related diet	4e-10
GCST004749_15	Lung cancer in ever smokers	7e-9
GCST010142_34	Fish- and plant-related diet	7e-9
GCST010142_35	Fish- and plant-related diet	8e-9
GCST010142_42	Fish- and plant-related diet	1e-8
GCST004749_16	Lung cancer in ever smokers	3e-8
GCST003518_34	Daytime sleep phenotypes	2e-7
GCST003901_17	Cognitive decline (age-related)	5e-6

EFO canonical traits (from GWAS)

7 canonical traits:

EFO ID	Trait name
EFO:0007828	daytime rest measurement
EFO:0004847	age at onset
EFO:0004509	hemoglobin measurement
EFO:0008111	diet measurement
EFO:0004614	apolipoprotein A 1 measurement
EFO:0004346	neuroimaging measurement
EFO:0008039	BMI-adjusted hip circumference

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (CPIC guideline: no)

CTD chemical–gene interactions

29 total (human), top 29 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
potassium chromate(VI)	decreases expression, affects cotreatment, increases expression	2
Benzo(a)pyrene	affects methylation, increases expression	2
bisphenol F	affects cotreatment, decreases methylation	1
urushiol	decreases expression	1
bisphenol A	decreases methylation	1
2,5,2’,5’-tetrachlorobiphenyl	increases expression	1
2-methyl-4-isothiazolin-3-one	increases expression	1
monobutyl phthalate	increases methylation, increases abundance	1
ferrous chloride	decreases expression	1
epigallocatechin gallate	affects cotreatment, increases expression	1
avobenzone	decreases expression	1
chromium hexavalent ion	affects expression	1
perfluorooctane sulfonic acid	increases expression	1
bisphenol S	affects cotreatment, decreases methylation	1
(+)-JQ1 compound	increases expression	1
Fulvestrant	affects cotreatment, decreases methylation	1
Air Pollutants	increases abundance, increases expression	1
Dimethyl Sulfoxide	increases expression	1
Formaldehyde	increases expression	1
Methyl Methanesulfonate	increases expression	1
Phthalic Acids	increases abundance, increases methylation	1
Quercetin	decreases expression	1
Tetrachlorodibenzodioxin	affects expression	1
Urethane	increases expression	1
Valproic Acid	increases expression	1
Cyclosporine	increases expression	1
Asbestos, Crocidolite	decreases methylation	1
Acrylamide	increases expression	1
Particulate Matter	increases abundance, increases expression	1

Clinical trials (associated diseases)

Via MONDO — disease-level, not drug-specific.