ARL13A

Summary

ARL13A (ARF like GTPase 13A, HGNC:31709) is a protein-coding gene on chromosome Xq22.1, encoding ADP-ribosylation factor-like protein 13A (Q5H913).

Predicted to enable GTP binding activity and GTPase activity. Predicted to be involved in non-motile cilium assembly and receptor localization to non-motile cilium. Predicted to be active in ciliary membrane; motile cilium; and non-motile cilium.

Source: NCBI Gene 392509 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 34 total — 5 pathogenic
• MANE Select transcript: NM_001162491

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:31709
Approved symbol	ARL13A
Name	ARF like GTPase 13A
Location	Xq22.1
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000174225
Ensembl biotype	protein_coding
OMIM	301144
Entrez	392509

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 2 protein_coding, 2 nonsense_mediated_decay

ENST00000372953, ENST00000450049, ENST00000450457, ENST00000494863

RefSeq mRNA: 1 — MANE Select: NM_001162491 NM_001162491

CCDS: CCDS55463

Canonical transcript exons

ENST00000450049 — 8 exons

Exon	Start	End
ENSE00000979178	100985667	100985916
ENSE00001335150	100988193	100988283
ENSE00001335151	100987390	100987556
ENSE00001335153	100986796	100986901
ENSE00001336570	100974127	100974197
ENSE00001459134	100973676	100973748
ENSE00002119397	100969708	100969809
ENSE00002209032	100990562	100990831

Expression profiles

Bgee: expression breadth ubiquitous, 129 present calls, max score 90.59.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0125 / max 10.4151, expressed in 3 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
196939	0.0125	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	90.59	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	86.82	gold quality
left testis	UBERON:0004533	78.59	gold quality
testis	UBERON:0000473	78.37	gold quality
right testis	UBERON:0004534	77.38	gold quality
mucosa of stomach	UBERON:0001199	61.66	gold quality
calcaneal tendon	UBERON:0003701	61.28	gold quality
right coronary artery	UBERON:0001625	58.19	gold quality
endometrium	UBERON:0001295	57.92	gold quality
granulocyte	CL:0000094	57.06	gold quality
leukocyte	CL:0000738	57.00	gold quality
monocyte	CL:0000576	56.74	gold quality
ectocervix	UBERON:0012249	55.62	gold quality
skin of abdomen	UBERON:0001416	55.56	gold quality
zone of skin	UBERON:0000014	55.31	gold quality
skin of leg	UBERON:0001511	55.11	gold quality
right ovary	UBERON:0002118	54.25	gold quality
rectum	UBERON:0001052	54.00	gold quality
descending thoracic aorta	UBERON:0002345	53.88	gold quality
popliteal artery	UBERON:0002250	53.86	gold quality
tibial artery	UBERON:0007610	53.83	gold quality
endocervix	UBERON:0000458	53.75	gold quality
uterine cervix	UBERON:0000002	53.63	gold quality
left ovary	UBERON:0002119	53.44	gold quality
fundus of stomach	UBERON:0001160	53.33	gold quality
right lung	UBERON:0002167	53.29	gold quality
ovary	UBERON:0000992	52.99	gold quality
skeletal muscle tissue	UBERON:0001134	52.87	gold quality
right adrenal gland cortex	UBERON:0035827	52.36	gold quality
ascending aorta	UBERON:0001496	52.15	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.10

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

15 targeting ARL13A, 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-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-545-3P	99.95	70.74	2783
HSA-MIR-2681-5P	99.75	67.64	1655
HSA-MIR-24-3P	99.59	69.97	1934
HSA-MIR-548B-3P	99.38	67.26	1000
HSA-MIR-148A-5P	99.30	68.27	1141
HSA-MIR-4263	99.18	69.25	2236
HSA-MIR-6738-3P	99.03	67.14	1326
HSA-MIR-5001-3P	98.91	67.28	1394
HSA-MIR-10A-5P	98.89	69.85	712
HSA-MIR-10B-5P	98.89	69.86	711
HSA-MIR-26B-3P	98.71	67.49	1102
HSA-MIR-323A-5P	98.59	65.13	651
HSA-MIR-8088	89.27	73.01	56

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	arl13a	ENSDARG00000052575
mus_musculus	Arl13a	ENSMUSG00000052549
rattus_norvegicus	Arl13a	ENSRNOG00000055454

Paralogs (30): ARF5 (ENSG00000004059), SAR1A (ENSG00000079332), ARFRP1 (ENSG00000101246), TRIM23 (ENSG00000113595), ARL6 (ENSG00000113966), ARL1 (ENSG00000120805), ARL4A (ENSG00000122644), ARL8B (ENSG00000134108), ARF3 (ENSG00000134287), ARL3 (ENSG00000138175), ARL5C (ENSG00000141748), ARF1 (ENSG00000143761), ARL8A (ENSG00000143862), ARL11 (ENSG00000152213), SAR1B (ENSG00000152700), ARL5A (ENSG00000162980), ARF6 (ENSG00000165527), ARL5B (ENSG00000165997), ARF4 (ENSG00000168374), ARL13B (ENSG00000169379), ARL10 (ENSG00000175414), ARL4D (ENSG00000175906), ARL14 (ENSG00000179674), ARL15 (ENSG00000185305), ARL17A (ENSG00000185829), ARL4C (ENSG00000188042), ARL9 (ENSG00000196503), ARL2 (ENSG00000213465), ARL16 (ENSG00000214087), ARL17B (ENSG00000228696)

Protein

Protein identifiers

ADP-ribosylation factor-like protein 13A — Q5H913 (reviewed: Q5H913)

Alternative names: ARF-like GTPase 13A

All UniProt accessions (3): Q5H913, H0YH34, J3KPB3

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the small GTPase superfamily. Arf family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q5H913-1	1	yes
Q5H913-2	2

RefSeq proteins (1): NP_001155963* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR006689	Small_GTPase_ARF/SAR	Family
IPR027417	P-loop_NTPase	Homologous_superfamily
IPR051995	Ciliary_GTPase	Family

Pfam: PF00025

UniProt features (6 total): binding site 3, chain 1, region of interest 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5H913-F1	70.91	0.51

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 (3): 28–35; 71–75; 130–133

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 48 (showing top): GOBP_PROTEIN_LOCALIZATION_TO_CILIUM, GOBP_PROTEIN_LOCALIZATION_TO_CELL_PERIPHERY, GOBP_CILIUM_ORGANIZATION, GOBP_ORGANELLE_ASSEMBLY, GOBP_PROTEIN_LOCALIZATION_TO_ORGANELLE, GOBP_CELL_PROJECTION_ORGANIZATION, GOBP_LOCALIZATION_WITHIN_MEMBRANE, GOCC_CELL_PROJECTION_MEMBRANE, GOCC_MOTILE_CILIUM, GOCC_PLASMA_MEMBRANE_REGION, GOCC_CILIARY_MEMBRANE, GOCC_CILIUM, GOMF_GTPASE_ACTIVITY, GOMF_HYDROLASE_ACTIVITY_ACTING_ON_ACID_ANHYDRIDES, chrXq22

GO Biological Process (2): receptor localization to non-motile cilium (GO:0097500), non-motile cilium assembly (GO:1905515)

GO Molecular Function (3): GTPase activity (GO:0003924), GTP binding (GO:0005525), nucleotide binding (GO:0000166)

GO Cellular Component (4): motile cilium (GO:0031514), ciliary membrane (GO:0060170), non-motile cilium (GO:0097730), cilium (GO:0005929)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cilium	3
protein localization to non-motile cilium	1
protein localization to ciliary membrane	1
cilium assembly	1
ribonucleoside triphosphate phosphatase activity	1
guanyl ribonucleotide binding	1
purine ribonucleoside triphosphate binding	1
nucleoside phosphate binding	1
heterocyclic compound binding	1
cell projection membrane	1
bounding membrane of organelle	1
intraciliary transport particle	1
membrane-bounded organelle	1
plasma membrane bounded cell projection	1

Protein interactions and networks

STRING

519 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ARL13A	ARL16	Q0P5N6	685
ARL13A	IFT88	Q13099	559
ARL13A	ARL10	Q8N8L6	548
ARL13A	NPHP4	O75161	513
ARL13A	KIF17	Q9P2E2	507
ARL13A	CYLC1	P35663	490
ARL13A	IFT27	Q9BW83	473
ARL13A	RAB23	Q9ULC3	464
ARL13A	KCTD9	Q7L273	462
ARL13A	BBS7	Q8IWZ6	447
ARL13A	CEP290	O15078	445
ARL13A	IFT20	Q8IY31	433
ARL13A	TCTN1	Q2MV58	432
ARL13A	SSTR3	P32745	430
ARL13A	EYA3	Q99504	425

IntAct

3 interactions, top by confidence:

A	B	Type	Score
ARL13A	NDUFAF7	psi-mi:“MI:0914”(association)	0.350

BioGRID (5): NDUFAF7 (Affinity Capture-MS), INTS12 (Affinity Capture-MS), NDUFAF7 (Affinity Capture-MS), INTS12 (Affinity Capture-MS), ARL13A (Positive Genetic)

ESM2 similar proteins: A0JMR6, A2RRS8, A6NFN9, A8MPX8, B1ANS9, O15297, O75747, P25022, P79457, Q08AW4, Q14680, Q14AW5, Q15052, Q2IBB1, Q2IBB4, Q2IBG0, Q2QL84, Q2QLH1, Q3MJ13, Q3US16, Q4R3G4, Q4R7Q1, Q5H913, Q5JTW2, Q5R5T0, Q5R6E1, Q5RFQ4, Q5SUS0, Q5XGI3, Q5XX13, Q5XXR3, Q692V3, Q6P2S7, Q6P3V7, Q7XVF9, Q86VS3, Q8BVT6, Q8C0W1, Q8C5W4, Q8IV35

Diamond homologs: A1CRG9, A1D4D1, A3LTA2, A8INQ0, A8ISN6, B5FYQ0, H2L0N8, O04266, O04267, O04834, O08697, O45379, P0C950, P0C951, P0CM16, P0CM17, P0CR30, P0CR31, P20606, P22274, P25160, P36404, P36405, P36536, P37996, P49703, P52885, P56559, P61208, Q01474, Q01475, Q02804, Q06849, Q09767, Q0CUN7, Q0VC18, Q10943, Q13795, Q19705, Q1MTE5

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	5
Likely pathogenic	0
Uncertain significance	14
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (5)

Variant ID	HGVS	Classification
151176	GRCh38/hg38 Xq21.31-22.1(chrX:91225162-101026774)x1	Pathogenic
151255	GRCh38/hg38 Xq21.33-22.3(chrX:95823036-104957737)x1	Pathogenic
2685000	GRCh37/hg19 Xq21.33-22.3(chrX:96349060-106950847)x3	Pathogenic
3391956	GRCh37/hg19 Xq21.2-22.3(chrX:84607697-104579525)x1	Pathogenic
395717	GRCh37/hg19 Xq22.1-22.2(chrX:99611312-103506684)	Pathogenic

SpliceAI

1236 predictions. Top by Δscore:

Variant	Effect	Δscore
X:100973666:A:AG	acceptor_gain	1.0000
X:100973667:A:G	acceptor_gain	1.0000
X:100973674:A:G	acceptor_gain	1.0000
X:100974203:GAAC:G	donor_gain	1.0000
X:100985660:T:G	acceptor_gain	1.0000
X:100985852:G:GT	donor_gain	1.0000
X:100985917:G:GG	donor_gain	1.0000
X:100986899:GTA:G	donor_gain	1.0000
X:100986902:G:GG	donor_gain	1.0000
X:100988191:A:AG	acceptor_gain	1.0000
X:100988191:A:G	acceptor_loss	1.0000
X:100988192:G:GG	acceptor_gain	1.0000
X:100988192:GC:G	acceptor_gain	1.0000
X:100988192:GCTT:G	acceptor_gain	1.0000
X:100988279:TACAG:T	donor_loss	1.0000
X:100988280:ACAG:A	donor_loss	1.0000
X:100988281:CAG:C	donor_loss	1.0000
X:100988282:AG:A	donor_loss	1.0000
X:100988283:GGT:G	donor_loss	1.0000
X:100988285:T:G	donor_loss	1.0000
X:100973668:T:G	acceptor_gain	0.9900
X:100973669:A:AG	acceptor_gain	0.9900
X:100973670:T:G	acceptor_gain	0.9900
X:100973671:TTAA:T	acceptor_loss	0.9900
X:100973672:TAA:T	acceptor_loss	0.9900
X:100973673:A:AG	acceptor_gain	0.9900
X:100973673:AAG:A	acceptor_loss	0.9900
X:100973674:A:AG	acceptor_loss	0.9900
X:100973675:G:GC	acceptor_loss	0.9900
X:100973675:G:GG	acceptor_gain	0.9900

AlphaMissense

1648 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
X:100986807:A:T	K131I	0.948
X:100985816:T:C	F94L	0.940
X:100985818:C:A	F94L	0.940
X:100985818:C:G	F94L	0.940
X:100986808:A:C	K131N	0.894
X:100986808:A:T	K131N	0.894
X:100985780:T:A	W82R	0.865
X:100985780:T:C	W82R	0.865
X:100985827:T:A	D97E	0.853
X:100985827:T:G	D97E	0.853
X:100987456:T:A	W185R	0.849
X:100987456:T:C	W185R	0.849
X:100986807:A:C	K131T	0.848
X:100985782:G:C	W82C	0.847
X:100985782:G:T	W82C	0.847
X:100985814:T:A	V93D	0.822
X:100985820:T:A	V95D	0.810
X:100987458:G:C	W185C	0.807
X:100987458:G:T	W185C	0.807
X:100985817:T:C	F94S	0.794
X:100985913:T:C	L126S	0.792
X:100974168:A:T	K34I	0.791
X:100985905:A:C	K123N	0.776
X:100985905:A:T	K123N	0.776
X:100985807:G:T	G91W	0.775
X:100985916:T:G	I127S	0.774
X:100986806:A:G	K131E	0.772
X:100985808:G:A	G91E	0.765
X:100985736:T:C	L67P	0.764
X:100985826:A:T	D97V	0.764

dbSNP variants (sampled 300 via entrez): RS1000276878 (X:100979953 GTCTC>G,GTCTCTC), RS1000497083 (X:100969027 A>G), RS1000608013 (X:100976532 C>T), RS1001309376 (X:100989917 G>A), RS1001361451 (X:100989386 C>G,T), RS1001448090 (X:100984476 A>T), RS1001832826 (X:100978664 G>A), RS1001858087 (X:100978121 G>A,C), RS1001922721 (X:100981384 T>C), RS1001924904 (X:100978836 T>C), RS1001929923 (X:100967912 G>A,T), RS1002044466 (X:100968494 G>A), RS1002312413 (X:100981448 G>A,C), RS1003652670 (X:100988056 G>T), RS1003660532 (X:100969594 G>A)

Disease associations

OMIM: gene MIM:301144 | disease phenotypes: MIM:300088, MIM:307200

GenCC curated gene-disease

Mondo (3): developmental and epileptic encephalopathy, 9 (MONDO:0010246), isolated growth hormone deficiency type III (MONDO:0010615), neurodevelopmental disorder (MONDO:0700092)

Orphanet (4): Female restricted epilepsy with intellectual disability (Orphanet:101039), X-linked intellectual disability-epilepsy syndrome (Orphanet:2076), Isolated growth hormone deficiency type III (Orphanet:231692), Non-acquired isolated growth hormone deficiency (Orphanet:631)

HPO phenotypes

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

GWAS associations

0 associations (top):

MeSH disease descriptors (3)

Descriptor	Name	Tree numbers
D065886	Neurodevelopmental Disorders	F03.625
C564715	Epilepsy, Female-Restricted, with Mental Retardation (supp.)
C537149	Hypogammaglobulinemia and Isolated growth hormone deficiency, X-linked (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

4 total (human), top 4 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
aristolochic acid I	increases expression	1
abrine	increases expression	1
Acetaminophen	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT04586348	PHASE4	UNKNOWN	Prenatal Iodine Supplementation and Early Childhood Neurodevelopment
NCT04873115	PHASE4	UNKNOWN	Double-blind, Placebo-controlled, Randomized Clinical Trial Comparing the Efficacy and Safety of Sialanar Plus orAl rehabiLitation Against Placebo Plus Oral Rehabilitation for chIldren and Adolescents With seVere Sialorrhoea and Neurodisabilties,
NCT02559102	PHASE3	COMPLETED	Dexmedetomidine Sedation Versus General Anaesthesia for Inguinal Hernia Surgery in Infants
NCT02757079	PHASE3	COMPLETED	Study of the Efficacy and Safety of NPC-15 for Sleep Disorders of Children With Neurodevelopmental Disorders
NCT06915480	PHASE3	RECRUITING	Reducing Missed Appointments
NCT07377032	PHASE3	RECRUITING	TAP-GRIN: Interventional Study on Patients With GRIN-related Neurodevelopmental Disorders
NCT02909959	PHASE2	COMPLETED	Sulforaphane for the Treatment of Young Men With Autism Spectrum Disorder
NCT06081348	PHASE2	RECRUITING	Sertraline vs. Placebo in the Treatment of Anxiety in Children and AdoLescents With NeurodevelopMental Disorders
NCT06352372	PHASE2	COMPLETED	Safety and Efficacy of tPBM for Epileptiform Activity in Autism
NCT00503191	PHASE1	COMPLETED	NeuroModulation Technique Treatment of Autism
NCT04475848	PHASE1	COMPLETED	A Study to Investigate the Safety, Tolerability, Pharmacokinetics, Pharmacodynamics and Food Effect of RO6953958 in Healthy Participants
NCT06300398	PHASE1	COMPLETED	IAMA-6 Oral Dose Study in Healthy Adults
NCT01783041	PHASE2/PHASE3	COMPLETED	Effect of Early L-Carnitine Supplementation on Neurodevelopmental Outcomes in Very Preterm Infants
NCT05767385	PHASE2/PHASE3	RECRUITING	Fetal Cerebrovascular Autoregulation in Congenital Heart Disease and Association With Neonatal Neurobehavior
NCT05675098	EARLY_PHASE1	NOT_YET_RECRUITING	Central Nervous System Stimulants and Physical Function in Children With Cerebral Palsy
NCT00783783	Not specified	COMPLETED	CYP2D6 Pharmacogenetics in Risperidone-Treated Children
NCT01778504	Not specified	RECRUITING	Studying Childhood-onset Behavioral, Psychiatric, and Developmental Disorders
NCT01850784	Not specified	UNKNOWN	High Energy Formula Feeding in Infants With Congenital Heart Disease
NCT01922791	Not specified	COMPLETED	Nutrition and Pregnancy Intervention Study
NCT01942525	Not specified	UNKNOWN	Influence of Intrauterine Growth Restriction on Amplitude-integrated EEG in Preterm Infants
NCT02003170	Not specified	COMPLETED	Etiology and Early Diagnosis of Neurodevelopmental Disorders
NCT02118649	Not specified	ACTIVE_NOT_RECRUITING	Enhancing Behavior and Brain Response to Visual Targets Using a Computer Game
NCT02557191	Not specified	TERMINATED	Biomarkers, Neurodevelopment and Preterm Infants
NCT02690675	Not specified	COMPLETED	Iron Supplement Effect on Child Development
NCT02694003	Not specified	COMPLETED	Better Nights, Better Days for Children With Neurodevelopment Disorders
NCT02792894	Not specified	COMPLETED	Family Networks (FaNs) for Children With Developmental Disorders and Delays
NCT02871674	Not specified	UNKNOWN	Good Night Project: Behavioural Sleep Interventions for Children With ADHD: A Randomised Controlled Trial
NCT02887157	Not specified	COMPLETED	Analyzing Retinal Microanatomy in ROP
NCT02898298	Not specified	COMPLETED	Positive Emotion Regulation Training in Children, Adolescents and Young Adults With and Without Developmental Disorder
NCT02912780	Not specified	UNKNOWN	Introduction of Microsystems in a Level 3 Neonatal Intensive Care Unit
NCT03023293	Not specified	COMPLETED	n-3 PUFAs, Irisin and Maternal Glucose Metabolism From Pregnancy to Postpartum
NCT03023644	Not specified	COMPLETED	Improving Neurodevelopmental Outcomes in Children With Congenital Heart Disease: An Intervention Study
NCT03032991	Not specified	UNKNOWN	Early Biomarkers of Neurodevelopment in Offspring of Diabetic Mothers
NCT03088189	Not specified	TERMINATED	Effect of Parental Peri-conceptional Vitamin B12 Supplementation on Infant Neurocognitive Development in Offspring
NCT03096028	Not specified	COMPLETED	Developmental Origins of Mental Health Disorders
NCT03148782	Not specified	COMPLETED	Brain Plasticity Underlying Acquisition of New Organizational Skills in Children-R61 Phase
NCT03172104	Not specified	COMPLETED	Neurobehavioural Development of Infants Born <30 Weeks Gestational Age Between Birth and Five Years of Age
NCT03222375	Not specified	RECRUITING	SQUED™ Series 28.1 Home-use and Treatment of Autowave Reverberator of Autism
NCT03229928	Not specified	COMPLETED	Clinical Testing of a Real-Time Behavior Measurement Tool: Measuring Outcomes for CHAnge
NCT03232489	Not specified	UNKNOWN	Study for the Evaluation of the Feasibility of Applying Advanced MRI Scanning in Pediatric Clinical Practice