CAPSL

Summary

CAPSL (calcyphosine like, HGNC:28375) is a protein-coding gene on chromosome 5p13.2, encoding Calcyphosin-like protein (Q8WWF8).

Predicted to enable calcium ion binding activity. Predicted to be located in cytoplasm.

Source: NCBI Gene 133690 — RefSeq curated summary.

At a glance

• GWAS associations: 14
• Clinical variants (ClinVar): 48 total
• Phenotypes (HPO): 1
• MANE Select transcript: NM_001042625

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28375
Approved symbol	CAPSL
Name	calcyphosine like
Location	5p13.2
Locus type	gene with protein product
Status	Approved
Aliases	MGC26610
Ensembl gene	ENSG00000152611
Ensembl biotype	protein_coding
OMIM	618799
Entrez	133690

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 6 protein_coding

ENST00000397366, ENST00000397367, ENST00000513623, ENST00000514524, ENST00000651391, ENST00000902317

RefSeq mRNA: 2 — MANE Select: NM_001042625 NM_001042625, NM_144647

CCDS: CCDS3912

Canonical transcript exons

ENST00000651391 — 5 exons

Exon	Start	End
ENSE00003844118	35920984	35921120
ENSE00003844970	35938541	35938622
ENSE00003847931	35904288	35904646
ENSE00003891161	35910366	35910543
ENSE00003896203	35909866	35910075

Expression profiles

Bgee: expression breadth ubiquitous, 113 present calls, max score 99.63.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.3859 / max 68.2200, expressed in 77 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
61289	0.3859	77

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
bronchial epithelial cell	CL:0002328	99.63	gold quality
bronchus	UBERON:0002185	99.02	gold quality
right uterine tube	UBERON:0001302	98.62	gold quality
oviduct epithelium	UBERON:0004804	97.32	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	96.51	gold quality
mucosa of paranasal sinus	UBERON:0005030	95.43	gold quality
caput epididymis	UBERON:0004358	93.26	gold quality
epithelium of nasopharynx	UBERON:0001951	92.79	gold quality
nasal cavity epithelium	UBERON:0005384	91.88	gold quality
fallopian tube	UBERON:0003889	89.13	gold quality
sperm	CL:0000019	82.39	gold quality
pituitary gland	UBERON:0000007	81.30	gold quality
nasal cavity mucosa	UBERON:0001826	80.15	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	80.06	gold quality
adenohypophysis	UBERON:0002196	79.96	gold quality
trachea	UBERON:0003126	79.64	gold quality
right lung	UBERON:0002167	75.49	gold quality
corpus epididymis	UBERON:0004359	74.95	gold quality
left testis	UBERON:0004533	74.89	gold quality
testis	UBERON:0000473	73.12	gold quality
adult organism	UBERON:0007023	72.84	gold quality
right testis	UBERON:0004534	72.63	gold quality
endometrium	UBERON:0001295	72.43	gold quality
kidney epithelium	UBERON:0004819	69.52	gold quality
cauda epididymis	UBERON:0004360	68.52	gold quality
hypothalamus	UBERON:0001898	67.93	gold quality
left ventricle myocardium	UBERON:0006566	65.72	gold quality
left uterine tube	UBERON:0001303	65.49	gold quality
cardiac muscle of right atrium	UBERON:0003379	65.24	gold quality
corpus callosum	UBERON:0002336	64.46	gold quality

Single-cell (SCXA)

Detected in 6 experiment(s), a significant marker in 6.

Experiment	Marker?	Max mean expression
E-CURD-114	yes	64.09
E-HCAD-1	yes	29.58
E-MTAB-10287	yes	27.77
E-GEOD-130148	yes	13.03
E-MTAB-9388	yes	7.13
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

17 targeting CAPSL, 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-574-5P	100.00	66.01	989
HSA-MIR-6764-5P	99.75	67.89	2304
HSA-MIR-1255A	99.74	68.09	744
HSA-MIR-1255B-5P	99.74	68.16	741
HSA-MIR-132-3P	99.73	70.56	1424
HSA-MIR-212-3P	99.73	70.65	1424
HSA-MIR-651-5P	99.64	68.49	1104
HSA-MIR-6719-3P	99.29	67.78	1387
HSA-MIR-3160-3P	99.07	64.78	955
HSA-MIR-511-5P	98.97	70.94	2268
HSA-MIR-5001-3P	98.91	67.28	1394
HSA-MIR-29B-1-5P	98.86	68.35	1364
HSA-MIR-8055	97.62	66.09	1023
HSA-MIR-505-5P	97.01	65.54	778
HSA-MIR-874-5P	96.93	63.92	1014
HSA-MIR-514A-3P	96.43	67.77	1048
HSA-MIR-514B-3P	96.43	67.77	1048

Literature-anchored findings (GeneRIF, showing 1)

• Calcyphosine-like (CAPSL) is regulated in Multiple Symmetric Lipomatosis and is involved in Adipogenesis. (PMID:31186450)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	capslb	ENSDARG00000003414
mus_musculus	Capsl	ENSMUSG00000039676
rattus_norvegicus	Capsl	ENSRNOG00000054277
drosophila_melanogaster	CG10126	FBGN0038088
drosophila_melanogaster	CG31345	FBGN0051345

Paralogs (5): CAPS (ENSG00000105519), PHF24 (ENSG00000122733), CAPS2 (ENSG00000180881), EFCAB6 (ENSG00000186976), SPATA21 (ENSG00000187144)

Protein

Protein identifiers

Calcyphosin-like protein — Q8WWF8 (reviewed: Q8WWF8)

All UniProt accessions (3): Q8WWF8, D6RF97, D6RHD7

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Cytoplasm.

RefSeq proteins (2): NP_001036090, NP_653248 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR002048	EF_hand_dom	Domain
IPR011992	EF-hand-dom_pair	Homologous_superfamily
IPR018247	EF_Hand_1_Ca_BS	Binding_site
IPR051581	Ca-bind	Family

Pfam: PF13499

UniProt features (18 total): binding site 10, domain 4, sequence variant 2, chain 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8WWF8-F1	91.88	0.76

Functional residue map

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

Ligand- & substrate-binding residues (10): 88; 90; 92; 94; 99; 52; 54; 56; 58; 63

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 82 (showing top): SENGUPTA_NASOPHARYNGEAL_CARCINOMA_DN, GOBP_BLOOD_VESSEL_MORPHOGENESIS, GOBP_VASCULOGENESIS, GOBP_SENSORY_ORGAN_DEVELOPMENT, GOBP_EPITHELIAL_CELL_PROLIFERATION, GOBP_RETINA_DEVELOPMENT_IN_CAMERA_TYPE_EYE, GOBP_CIRCULATORY_SYSTEM_DEVELOPMENT, GOBP_TUBE_MORPHOGENESIS, DODD_NASOPHARYNGEAL_CARCINOMA_DN, GOBP_SENSORY_SYSTEM_DEVELOPMENT, GSE13522_CTRL_VS_T_CRUZI_G_STRAIN_INF_SKIN_UP, GOBP_TUBE_DEVELOPMENT, PRKDC_TARGET_GENES, GSE10240_CTRL_VS_IL17_AND_IL22_STIM_PRIMARY_BRONCHIAL_EPITHELIAL_CELLS_UP, CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_2

GO Biological Process (0):

GO Molecular Function (2): calcium ion binding (GO:0005509), metal ion binding (GO:0046872)

GO Cellular Component (2): cytoplasm (GO:0005737), organelle (GO:0043226)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	2
metal ion binding	1
cation binding	1
intracellular anatomical structure	1

Protein interactions and networks

STRING

1107 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CAPSL	EFHB	Q8N7U6	507
CAPSL	LMBRD2	Q68DH5	456
CAPSL	IQCJ	Q1A5X6	430
CAPSL	POU2AF2	Q8IXP5	411
CAPSL	EXOC3L4	Q17RC7	395
CAPSL	CLEC16A	Q2KHT3	391
CAPSL	SPEF2	Q9C093	383
CAPSL	JAKMIP2	Q96AA8	379
CAPSL	CIMAP3	Q8TCI5	376
CAPSL	CFAP263	Q9H0I3	373
CAPSL	IL7R	P16871	371
CAPSL	TMEM39A	Q9NV64	365
CAPSL	RAI2	Q9Y5P3	365
CAPSL	DEPDC1B	Q8WUY9	364
CAPSL	ADAD1	Q96M93	359

IntAct

4 interactions, top by confidence:

A	B	Type	Score
CAPSL	DLGAP5	psi-mi:“MI:0914”(association)	0.530
CAPSL	TUBA1B	psi-mi:“MI:0914”(association)	0.350
CAPSL	LCN1	psi-mi:“MI:0914”(association)	0.350

BioGRID (15): CAPSL (Synthetic Lethality), DLGAP5 (Affinity Capture-MS), TUBB2A (Affinity Capture-MS), TUBB4B (Affinity Capture-MS), BIRC6 (Affinity Capture-MS), TUBB8 (Affinity Capture-MS), TUBA1A (Affinity Capture-MS), TUBA1B (Affinity Capture-MS), EML4 (Affinity Capture-MS), TUBA1C (Affinity Capture-MS), TUBB3 (Affinity Capture-MS), NEDD8-MDP1 (Affinity Capture-MS), LCN1 (Affinity Capture-MS), DDX46 (Cross-Linking-MS (XL-MS)), APP (Reconstituted Complex)

ESM2 similar proteins: A0PJX0, A1L1L6, A4IG32, B1A8Z2, B1H2N3, C7A278, D2HZB0, O88456, P04632, P06813, P07090, P22676, P47728, Q08331, Q0IIL1, Q17QE5, Q1RMX9, Q2HJF8, Q2KI69, Q32L26, Q32LU1, Q3T0E8, Q3ZBY3, Q4R518, Q5PPL2, Q5RDF9, Q5ZM73, Q6NVC5, Q6P6Q9, Q6P8Y1, Q6PHZ8, Q6PIL6, Q8BG51, Q8HYN7, Q8IXI2, Q8R426, Q8VCX5, Q8WWF8, Q99828, Q99MG9

Diamond homologs: P10463, P41150, P80363, P80364, Q0VCC0, Q13938, Q6P8Y1, Q8WWF8, Q9GKR6, P82978, Q03975, Q3E9C0, Q66L49, Q8BUG5, Q9FMP5, Q9S9V0, Q9BXY5

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	41
Likely benign	0
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

979 predictions. Top by Δscore:

Variant	Effect	Δscore
5:35909860:ACTT:A	donor_loss	1.0000
5:35909861:CTT:C	donor_loss	1.0000
5:35909862:TTA:T	donor_loss	1.0000
5:35909863:TA:T	donor_loss	1.0000
5:35909864:ACCA:A	donor_loss	1.0000
5:35910071:GGAGG:G	acceptor_gain	1.0000
5:35910076:C:CC	acceptor_gain	1.0000
5:35910362:TTACT:T	donor_loss	1.0000
5:35910363:TA:T	donor_loss	1.0000
5:35910364:A:AC	donor_gain	1.0000
5:35910364:ACT:A	donor_gain	1.0000
5:35910365:C:CT	donor_gain	1.0000
5:35910365:CT:C	donor_gain	1.0000
5:35910365:CTC:C	donor_gain	1.0000
5:35910365:CTCTT:C	donor_gain	1.0000
5:35910540:CACT:C	acceptor_gain	1.0000
5:35910542:CT:C	acceptor_gain	1.0000
5:35922062:CAATG:C	acceptor_gain	1.0000
5:35922066:G:C	acceptor_gain	1.0000
5:35922066:G:GC	acceptor_gain	1.0000
5:35922070:A:T	acceptor_gain	1.0000
5:35906395:A:T	acceptor_gain	0.9900
5:35909864:A:AC	donor_gain	0.9900
5:35909865:C:CC	donor_gain	0.9900
5:35909865:CCAAT:C	donor_gain	0.9900
5:35910072:GAGG:G	acceptor_gain	0.9900
5:35910073:AGG:A	acceptor_gain	0.9900
5:35910073:AGGCT:A	acceptor_gain	0.9900
5:35910074:GG:G	acceptor_gain	0.9900
5:35910074:GGCT:G	acceptor_gain	0.9900

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000171258 (5:35915773 A>G,T), RS1000220533 (5:35920751 C>G,T), RS1000377286 (5:35930780 G>A), RS1000386390 (5:35920928 C>G), RS1000438761 (5:35920676 G>A,T), RS1000598291 (5:35925166 C>T), RS1000787275 (5:35926319 A>G), RS1000877503 (5:35930792 T>C), RS1000891320 (5:35908674 T>C), RS1000988086 (5:35913279 A>G), RS1001066378 (5:35940461 G>A), RS1001154998 (5:35919517 G>A,T), RS1001241491 (5:35937272 T>C), RS1001354676 (5:35906237 C>T), RS1001381289 (5:35924999 C>G)

Disease associations

OMIM: gene MIM:618799 | disease phenotypes: MIM:209850

GenCC curated gene-disease

Mondo (1): autism (MONDO:0005260)

Orphanet (0):

HPO phenotypes

1 total (1 of 1 shown, HPO-id order):

HPO	Term
HP:0000717	Autism

GWAS associations

14 associations (top):

Study	Trait	p-value
GCST000038_3	Type 1 diabetes	8.000000e-06
GCST003129_22	Primary biliary cholangitis	5.000000e-11
GCST003184_13	Atopic dermatitis	2.000000e-10
GCST003184_5	Atopic dermatitis	3.000000e-14
GCST005581_3	Primary biliary cirrhosis	2.000000e-13
GCST006409_29	Allergic rhinitis	4.000000e-32
GCST007036_3	Primary biliary cholangitis	2.000000e-09
GCST007563_11	Allergic disease (asthma, hay fever or eczema)	3.000000e-15
GCST007564_36	Asthma or allergic disease (pleiotropy)	2.000000e-14
GCST007798_69	Asthma	2.000000e-13
GCST007799_44	Asthma (adult onset)	9.000000e-14
GCST008916_32	Asthma	1.000000e-10
GCST011096_29	Systemic lupus erythematosus	4.000000e-08
GCST90014325_47	Asthma	5.000000e-10

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:1002011	adult onset asthma

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
D001321	Autistic Disorder	F03.625.164.113.500

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

15 total (human), top 15 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol A	decreases expression, decreases methylation	2
Air Pollutants	decreases expression, increases abundance, increases expression	2
Valproic Acid	decreases methylation, increases expression	2
Aflatoxin B1	decreases methylation, increases methylation	2
perfluorooctanoic acid	increases expression	1
potassium chromate(VI)	increases expression	1
S-(1,2-dichlorovinyl)cysteine	decreases reaction, increases expression	1
2,3,5-trichloro-6-phenyl-(1,4)benzoquinone	increases expression	1
Aspirin	increases expression	1
Benzo(a)pyrene	decreases methylation, increases methylation, affects methylation	1
Lipopolysaccharides	increases expression, decreases reaction	1
Phenobarbital	decreases expression	1
Smoke	increases abundance, increases expression	1
Tobacco Smoke Pollution	decreases expression	1
Particulate Matter	increases abundance, decreases expression	1

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT00211796	PHASE4	COMPLETED	Divalproex Sodium ER in Adult Autism
NCT00391261	PHASE4	COMPLETED	An Open-label Trial of Metformin for Weight Control of Pediatric Patients on Antipsychotic Medications.
NCT00409747	PHASE4	COMPLETED	Minocycline to Treat Childhood Regressive Autism
NCT00576732	PHASE4	COMPLETED	A Study of the Effectiveness and Safety of Two Doses of Risperidone in the Treatment of Children and Adolescents With Autistic Disorder
NCT00844753	PHASE4	COMPLETED	Atomoxetine, Placebo and Parent Management Training in Autism
NCT01028820	PHASE4	COMPLETED	FMRI Brain Activation of Aripiprazole Treatment in Autism Spectrum Disorders
NCT01098383	PHASE4	UNKNOWN	Treatment With Acetyl-Choline Esterase Inhibitors in Children With Autism Spectrum Disorders
NCT01333865	PHASE4	COMPLETED	A Study of Memantine Hydrochloride (Namenda®) for Cognitive and Behavioral Impairment in Adults With Autism Spectrum Disorders
NCT01337700	PHASE4	COMPLETED	Milnacipran in Autism and the Functional Locus Coeruleus and Noradrenergic Model of Autism
NCT01695200	PHASE4	COMPLETED	Omega-3 Fatty Acids in Autism Spectrum Disorders
NCT02069977	PHASE4	UNKNOWN	Study to Evaluate the Efficacy and Safety of Aripiprazole
NCT02096952	PHASE4	COMPLETED	Methylphenidate ER Liquid Formulation in Adults With ASD and ADHD
NCT02199925	PHASE4	UNKNOWN	An Open-Label Study to Evaluate the Efficacy of High-Dose Gammaplex in Children on the Autism Spectrum
NCT02235467	PHASE4	COMPLETED	Multisite Study: Parental Training Using Video Modelling to Develop Social Skills in Children With Autism
NCT02255565	PHASE4	COMPLETED	Dose Response Effects of Quillivant XR in Children With ADHD and Autism: A Pilot Study
NCT02940574	PHASE4	COMPLETED	Neural and Behavioral Effects of Oxytocin in Autism Spectrum Disorders
NCT03333629	PHASE4	COMPLETED	Promoting Positive Outcomes for Individuals With ASD: Linking Early Detection, Treatment, and Long-term Outcomes
NCT03337646	PHASE4	COMPLETED	Evaluation of the Effect and Safety of Lisdexamfetamine in Children Aged 6-12 With ADHD and Autism
NCT03538431	PHASE4	COMPLETED	Improving Driving in Young People With Autism Spectrum Disorders
NCT03757585	PHASE4	COMPLETED	Natural Treatments for the Management of Emotional Dysregulation in Youth With Non-verbal Learning Disability (NVLD) and/or Autism Spectrum Disorders (ASD)
NCT04903353	PHASE4	COMPLETED	Pragmatic Trial Comparing Weight Gain in Children With Autism Taking Risperidone Versus Aripiprazole
NCT05063656	PHASE4	COMPLETED	Biomarker-Driven Pharmacological Treatment of Adolescents With Autism Spectrum Disorder With Gabapentin
NCT05146245	PHASE4	UNKNOWN	Safety and Pharmacokinetics of Antipsychotics in Children 2: Studying TDM in an RCT
NCT05916339	PHASE4	RECRUITING	AWARE: Management of ADHD in Autism Spectrum Disorder
NCT05954052	PHASE4	TERMINATED	A Study of Glutathione in Children With Autism Spectrum Disorder
NCT06853665	PHASE4	RECRUITING	The TEAM Study - Treatment Efficacy for Autism/Attention Using Mixed Amphetamine
NCT07054697	PHASE4	COMPLETED	Pilot-RCT With Individualized Homeopathic Treatment in the Children With Autism Spectrum Disorder
NCT07161804	PHASE4	COMPLETED	Pilot RCT Using Homeopathic Medicines in ASD
NCT07439042	PHASE4	NOT_YET_RECRUITING	Buspirone for Anxiety in Autistic Youth
NCT00036231	PHASE3	TERMINATED	Synthetic Human Secretin in Children With Autism and Gastrointestinal Dysfunction
NCT00036244	PHASE3	COMPLETED	Synthetic Human Secretin in Children With Autism
NCT00065884	PHASE3	UNKNOWN	Valproate Response in Aggressive Autistic Adolescents
NCT00065962	PHASE3	COMPLETED	Secretin for the Treatment of Autism
NCT00252603	PHASE3	COMPLETED	Galantamine Versus Placebo in Childhood Autism
NCT00346736	PHASE3	COMPLETED	Use of Acupuncture In Children With Autistic Spectrum Disorder
NCT00352248	PHASE3	COMPLETED	Randomized Controlled Trial of Acupuncture Versus Sham Acupuncture in Autistic Spectrum Disorder
NCT00352352	PHASE3	COMPLETED	Use of Acupuncture In Children With Autistic Spectrum Disorder
NCT00355329	PHASE3	COMPLETED	Randomized Control Trial of Using Tongue Acupuncture in Autistic Spectrum Disorder Using PET Scan for Clinical Correlation
NCT00498173	PHASE3	COMPLETED	Effectiveness of Atomoxetine in Treating ADHD Symptoms in Children and Adolescents With Autism
NCT00541346	PHASE3	COMPLETED	A Pilot Study of Daytrana TM in Children With Autism Co-Morbid for Attention Deficit Hyperactivity Disorder (ADHD) Symptoms