RSPRY1

gene
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Also known as KIAA1972

Summary

RSPRY1 (ring finger and SPRY domain containing 1, HGNC:29420) is a protein-coding gene on chromosome 16q13, encoding RING finger and SPRY domain-containing protein 1 (Q96DX4).

This gene encodes a glycoprotein that contains a RING-type zinc finger domain and an SPRY domain of unknown function. Alternative splicing of this gene results in multiple transcript variants.

Source: NCBI Gene 89970 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): progressive spondyloepimetaphyseal dysplasia-short stature-short fourth metatarsals-intellectual disability syndrome (Strong, GenCC)
  • GWAS associations: 3
  • Clinical variants (ClinVar): 211 total — 5 pathogenic, 1 likely-pathogenic
  • Phenotypes (HPO): 82
  • MANE Select transcript: NM_133368

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:29420
Approved symbolRSPRY1
Namering finger and SPRY domain containing 1
Location16q13
Locus typegene with protein product
StatusApproved
AliasesKIAA1972
Ensembl geneENSG00000159579
Ensembl biotypeprotein_coding
OMIM616585
Entrez89970

Gene structure

Transcript identifiers

Ensembl transcripts: 34 — 29 protein_coding, 4 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000394420, ENST00000537866, ENST00000561641, ENST00000562439, ENST00000562768, ENST00000562959, ENST00000563073, ENST00000564435, ENST00000564530, ENST00000566352, ENST00000568505, ENST00000568920, ENST00000860800, ENST00000860801, ENST00000860802, ENST00000860803, ENST00000860804, ENST00000860805, ENST00000860806, ENST00000860807, ENST00000860808, ENST00000860809, ENST00000935122, ENST00000935123, ENST00000935124, ENST00000935125, ENST00000935126, ENST00000935127, ENST00000970574, ENST00000970575, ENST00000970576, ENST00000970577, ENST00000970578, ENST00000970579

RefSeq mRNA: 4 — MANE Select: NM_133368 NM_001305163, NM_001305164, NM_001305182, NM_133368

CCDS: CCDS10775

Canonical transcript exons

ENST00000394420 — 15 exons

ExonStartEnd
ENSE000010464995722073257220847
ENSE000010465055721610757216173
ENSE000015184085718632957186451
ENSE000025839645723887957240469
ENSE000027086585720450457205008
ENSE000034683995720907557209187
ENSE000034999895722127257221415
ENSE000035088185723116757231319
ENSE000035168615720805857208110
ENSE000035984335721690457217035
ENSE000036120045723512457235228
ENSE000036262725723071157230813
ENSE000036313835721297257213098
ENSE000036345275722734257227453
ENSE000036530015721388857213946

Expression profiles

Bgee: expression breadth ubiquitous, 256 present calls, max score 98.81.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 18.5106 / max 101.0023, expressed in 1812 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
15431815.87941809
1543192.48651384
1543170.144738

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
kidney epitheliumUBERON:000481998.81gold quality
nasal cavity epitheliumUBERON:000538497.06gold quality
secondary oocyteCL:000065596.20gold quality
mucosa of paranasal sinusUBERON:000503096.12gold quality
ileal mucosaUBERON:000033196.01gold quality
oocyteCL:000002394.98gold quality
spermCL:000001994.97gold quality
jejunal mucosaUBERON:000039994.20gold quality
cardia of stomachUBERON:000116294.16gold quality
upper arm skinUBERON:000426393.87gold quality
epithelial cell of pancreasCL:000008393.85gold quality
ganglionic eminenceUBERON:000402393.79gold quality
nippleUBERON:000203092.78gold quality
ventricular zoneUBERON:000305392.78gold quality
myocardiumUBERON:000234992.67silver quality
tibialis anteriorUBERON:000138592.64gold quality
cortical plateUBERON:000534392.50gold quality
adrenal tissueUBERON:001830392.45gold quality
epithelium of mammary glandUBERON:000324492.33gold quality
mammary ductUBERON:000176592.28gold quality
colonic mucosaUBERON:000031792.26gold quality
bronchial epithelial cellCL:000232892.14gold quality
vena cavaUBERON:000408792.13silver quality
bronchusUBERON:000218592.08gold quality
cartilage tissueUBERON:000241892.05gold quality
cardiac muscle of right atriumUBERON:000337992.01silver quality
lower lobe of lungUBERON:000894991.99gold quality
mammalian vulvaUBERON:000099791.79gold quality
endometriumUBERON:000129591.79gold quality
oviduct epitheliumUBERON:000480491.78gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes7.46

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

114 targeting RSPRY1, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-5011-5P100.0083.465820
HSA-MIR-6867-5P100.0082.213464
HSA-MIR-190A-3P100.0080.355520
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-5193100.0067.261744
HSA-MIR-6759-5P99.9966.54785
HSA-MIR-33A-5P99.9968.621055
HSA-MIR-33B-5P99.9968.581062
HSA-MIR-548AN99.9770.912817
HSA-MIR-314899.9775.066478
HSA-MIR-548AJ-3P99.9673.385345
HSA-MIR-548X-3P99.9673.385345
HSA-MIR-365899.9673.874379
HSA-MIR-568899.9673.234504
HSA-MIR-495-3P99.9672.814197
HSA-MIR-548J-3P99.9472.614881
HSA-MIR-548AE-3P99.9372.664867
HSA-MIR-548AH-3P99.9372.544872
HSA-MIR-548AM-3P99.9372.544872
HSA-MIR-548AQ-3P99.9372.664867
HSA-MIR-129799.9173.413162
HSA-MIR-130599.9171.433443
HSA-MIR-368699.9070.532432
HSA-MIR-6783-3P99.8967.922059
HSA-MIR-1343-3P99.8966.781815
HSA-MIR-548D-3P99.8770.674362
HSA-MIR-548BB-3P99.8670.584354
HSA-MIR-548AC99.8470.774351
HSA-MIR-548H-3P99.8470.804349
HSA-MIR-548Z99.8470.804349

Literature-anchored findings (GeneRIF, showing 3)

  • RSPRY1 Mutations are associated with Progressive Skeletal Dysplasia. (PMID:26365341)
  • we provide further evidence that Spondyloepimetaphyseal dysplasia Faden-Alkuraya type is a RSPRY1-associated skeletal dysplasia with a distinctive phenotype composed of spondyloepimetaphyseal dysplasia, cono-brachydactyly, and craniosynostosis along with recognizable facial features and intellectual disability. (PMID:30063090)
  • Two sisters with RSPRY1-related spondyloepimetaphyseal dysplasia. (PMID:38562122)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_reriorspry1ENSDARG00000062558
mus_musculusRspry1ENSMUSG00000050079
rattus_norvegicusRspry1ENSRNOG00000060931
caenorhabditis_elegansF16A11.1WBGENE00008876

Paralogs (1): RNF123 (ENSG00000164068)

Protein

Protein identifiers

RING finger and SPRY domain-containing protein 1Q96DX4 (reviewed: Q96DX4)

All UniProt accessions (5): Q96DX4, H3BPL2, H3BQG6, H3BQQ7, H3BSC7

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Secreted.

Disease relevance. Spondyloepimetaphyseal dysplasia, Faden-Alkuraya type (SEMDFA) [MIM:616723] An autosomal recessive skeletal disorder characterized by spondyloepimetaphyseal dysplasia, short stature, facial dysmorphism, short fourth metatarsals, and intellectual disability. The disease is caused by variants affecting the gene represented in this entry.

Isoforms (2)

UniProt IDNamesCanonical?
Q96DX4-11yes
Q96DX4-22

RefSeq proteins (3): NP_001292092, NP_001292093, NP_588609* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001841Znf_RINGDomain
IPR001870B30.2/SPRYDomain
IPR003877SPRY_domDomain
IPR013083Znf_RING/FYVE/PHDHomologous_superfamily
IPR013320ConA-like_dom_sfHomologous_superfamily
IPR016024ARM-type_foldHomologous_superfamily
IPR035774SPRY_RSPRY1Domain
IPR043136B30.2/SPRY_sfHomologous_superfamily
IPR045129RNF123/RKP/RSPRY1Family

Pfam: PF00622, PF13920

UniProt features (12 total): splice variant 2, compositionally biased region 2, signal peptide 1, chain 1, sequence variant 1, domain 1, zinc finger region 1, region of interest 1, modified residue 1, glycosylation site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q96DX4-F184.780.74

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 (1): 50

Glycosylation sites (1): 314

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 340 (showing top): RNGTGGGC_UNKNOWN, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, COUP_01, MILI_PSEUDOPODIA_HAPTOTAXIS_UP, USF_01, TGIF_01, ZIC1_01, GGGNNTTTCC_NFKB_Q6_01, HNF4_01, AACTTT_UNKNOWN, USF_02, MARTINEZ_RESPONSE_TO_TRABECTEDIN_DN, EGR1_01, GOBP_PROTEIN_CATABOLIC_PROCESS, TGGAAA_NFAT_Q4_01

GO Biological Process (1): obsolete proteolysis involved in protein catabolic process (GO:0051603)

GO Molecular Function (4): ubiquitin-protein transferase activity (GO:0004842), zinc ion binding (GO:0008270), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (2): extracellular region (GO:0005576), cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure2
ubiquitin-like protein transferase activity1
transition metal ion binding1
binding1
cation binding1
intracellular anatomical structure1

Protein interactions and networks

STRING

756 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
RSPRY1CCDC106Q9BWC9595
RSPRY1EAF1Q96JC9593
RSPRY1CLXNQ9HAE3576
RSPRY1GPATCH3Q96I76570
RSPRY1PRR23CQ6ZRP0567
RSPRY1FIZ1Q96SL8562
RSPRY1ZC3H15Q8WU90557
RSPRY1NUDT13Q86X67557
RSPRY1ZNRF2Q8NHG8533
RSPRY1MRPS34P82930528
RSPRY1TPRA1Q86W33528
RSPRY1METTL6Q8TCB7525
RSPRY1SNX20Q7Z614499
RSPRY1NELFBQ8WX92492
RSPRY1FBXO9Q9UK97490

IntAct

96 interactions, top by confidence:

ABTypeScore
VIMNEFLpsi-mi:“MI:0914”(association)0.840
UNC119UNC119Bpsi-mi:“MI:0914”(association)0.640
HEY2ARL10psi-mi:“MI:0914”(association)0.640
LYPD3SCAMP1psi-mi:“MI:0914”(association)0.640
VDAC1HK1psi-mi:“MI:0914”(association)0.560
SLC15A1METTL15psi-mi:“MI:0914”(association)0.530
GCNT3BCKDKpsi-mi:“MI:0914”(association)0.530
CDK5R1DENRpsi-mi:“MI:0914”(association)0.530
ITM2ANDUFB5psi-mi:“MI:0914”(association)0.530
SPINK2STRNpsi-mi:“MI:0914”(association)0.530
WNT7ALDLRpsi-mi:“MI:0914”(association)0.530
RSPRY1NEFLpsi-mi:“MI:0914”(association)0.530
SPATA19MTHFRpsi-mi:“MI:0914”(association)0.530
FBLZNF316psi-mi:“MI:0914”(association)0.530
CLEC3AZZEF1psi-mi:“MI:0914”(association)0.530
CCNJLHSPA5psi-mi:“MI:0914”(association)0.530
XAGE3WIZpsi-mi:“MI:0914”(association)0.530
IL1R2EXOC5psi-mi:“MI:0914”(association)0.530

BioGRID (124): RSPRY1 (Affinity Capture-MS), RSPRY1 (Affinity Capture-MS), RSPRY1 (Affinity Capture-MS), RSPRY1 (Affinity Capture-MS), RSPRY1 (Affinity Capture-MS), RSPRY1 (Affinity Capture-MS), RSPRY1 (Affinity Capture-MS), RSPRY1 (Synthetic Lethality), INF2 (Affinity Capture-MS), C5orf30 (Affinity Capture-MS), NES (Affinity Capture-MS), INA (Affinity Capture-MS), RSPRY1 (Affinity Capture-MS), RSPRY1 (Affinity Capture-MS), RSPRY1 (Affinity Capture-MS)

ESM2 similar proteins: A1L0Y2, A2ALK8, A2ARP1, A2Z8S0, A4IFG2, A8XT88, B1AVZ0, B3M1E1, B3P4N5, B4GZ20, B4HJC0, B4KA23, B4LVS8, B4NKI9, B4PVH6, B4QVW6, M9MRI4, O35242, O76050, P0C644, P26045, Q18223, Q29B63, Q29RQ5, Q3MHZ2, Q3UJK4, Q571F5, Q5M870, Q5NCX5, Q5PQR3, Q5R881, Q6PFW1, Q6PJ21, Q75G68, Q8BVR6, Q8C726, Q8CJC5, Q8R516, Q91YL3, Q91ZY8

Diamond homologs: A0A5F9C6I2, A1L252, A2VD92, B0LPN4, D3ZXK7, E9PZQ0, E9Q401, F1LMY4, O94712, P11716, P16960, P21817, P30957, P69566, Q15413, Q19614, Q1LUS8, Q28FM1, Q5R881, Q5XH91, Q5XPI3, Q5XPI4, Q6VN19, Q8BVR6, Q90WU3, Q92736, Q95LP3, Q96DX4, Q96S59, Q9PTY5, Q9VNV3, A1E2V0, A1L020, A1L3F4, A5D8Q0, A9JTP3, A9ULZ2, D3ZDI6, E3SCZ8, O08863

SIGNOR signaling

1 interactions.

AEffectBMechanism
Ub:E2“up-regulates activity”RSPRY1ubiquitination

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic5
Likely pathogenic1
Uncertain significance67
Likely benign109
Benign19

Top pathogenic / likely-pathogenic (6)

Variant IDHGVSClassification
1029071NM_133368.3(RSPRY1):c.1422T>A (p.Cys474Ter)Pathogenic
1706547NM_133368.3(RSPRY1):c.358G>T (p.Glu120Ter)Pathogenic
218885NM_133368.3(RSPRY1):c.1279dup (p.Thr427fs)Pathogenic
218886NM_133368.3(RSPRY1):c.121G>T (p.Gly41Cys)Pathogenic
2427211NC_000016.9:g.(?57242967)(57243119_?)delPathogenic
3391106NM_133368.3(RSPRY1):c.901_901+15delLikely pathogenic

SpliceAI

2429 predictions. Top by Δscore:

VariantEffectΔscore
16:57207551:A:AGacceptor_gain1.0000
16:57209073:A:AGacceptor_gain1.0000
16:57209074:G:GGacceptor_gain1.0000
16:57209188:G:GGdonor_gain1.0000
16:57212966:TTTTA:Tacceptor_loss1.0000
16:57212967:TTTA:Tacceptor_loss1.0000
16:57212968:TTA:Tacceptor_loss1.0000
16:57212969:TAG:Tacceptor_loss1.0000
16:57212970:A:AGacceptor_gain1.0000
16:57212970:A:Tacceptor_loss1.0000
16:57212970:AG:Aacceptor_gain1.0000
16:57212971:G:Aacceptor_loss1.0000
16:57212971:G:GGacceptor_gain1.0000
16:57212971:GG:Gacceptor_gain1.0000
16:57212971:GGAT:Gacceptor_gain1.0000
16:57213094:AGCAG:Adonor_loss1.0000
16:57213096:CAGG:Cdonor_loss1.0000
16:57213097:AG:Adonor_loss1.0000
16:57213098:GGT:Gdonor_loss1.0000
16:57213099:G:GCdonor_loss1.0000
16:57213100:T:Adonor_loss1.0000
16:57214161:C:Gdonor_gain1.0000
16:57216169:GACAA:Gdonor_gain1.0000
16:57216174:G:GGdonor_gain1.0000
16:57216995:TC:Tdonor_gain1.0000
16:57217036:G:GGdonor_gain1.0000
16:57220730:A:AGacceptor_gain1.0000
16:57220731:G:GAacceptor_gain1.0000
16:57220847:GGTA:Gdonor_loss1.0000
16:57220849:T:Gdonor_loss1.0000

AlphaMissense

3797 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
16:57204981:T:CL108P1.000
16:57204990:T:AI111K1.000
16:57204999:T:CL114P1.000
16:57208090:T:CL128S1.000
16:57208101:G:CA132P1.000
16:57209083:T:AW138R1.000
16:57209083:T:CW138R1.000
16:57209085:G:CW138C1.000
16:57209085:G:TW138C1.000
16:57209096:T:AV142D1.000
16:57209137:G:AG156R1.000
16:57209137:G:CG156R1.000
16:57209138:G:AG156E1.000
16:57209144:C:AA158D1.000
16:57209147:T:AV159D1.000
16:57209156:T:CL162S1.000
16:57209162:T:CL164P1.000
16:57209170:T:CC167R1.000
16:57209179:C:TP170S1.000
16:57209180:C:AP170H1.000
16:57213058:C:AN201K1.000
16:57213058:C:GN201K1.000
16:57213069:T:AV205D1.000
16:57213084:C:AA210D1.000
16:57213093:T:CL213P1.000
16:57213098:G:CG215R1.000
16:57213888:G:AG215D1.000
16:57217017:T:AW295R1.000
16:57217017:T:CW295R1.000
16:57220822:T:CL331P1.000

dbSNP variants (sampled 300 via entrez): RS1000131739 (16:57226920 A>G), RS1000159032 (16:57219935 T>C), RS1000256645 (16:57186918 C>G,T), RS1000406513 (16:57212931 G>A), RS1000628241 (16:57198509 T>C), RS1000637311 (16:57192152 G>A), RS1000731564 (16:57189540 C>A), RS1000772954 (16:57192463 A>C,G), RS1000887990 (16:57186140 C>T), RS1000936795 (16:57198222 A>G), RS1001137482 (16:57200965 A>C,G,T), RS1001189925 (16:57204511 A>G,T), RS1001304932 (16:57202680 C>T), RS1001320634 (16:57195104 T>C), RS1001382815 (16:57186273 A>C)

Disease associations

OMIM: gene MIM:616585 | disease phenotypes: MIM:616723

GenCC curated gene-disease

DiseaseClassificationInheritance
progressive spondyloepimetaphyseal dysplasia-short stature-short fourth metatarsals-intellectual disability syndromeStrongAutosomal recessive

Mondo (1): progressive spondyloepimetaphyseal dysplasia-short stature-short fourth metatarsals-intellectual disability syndrome (MONDO:0014748)

Orphanet (1): Progressive spondyloepimetaphyseal dysplasia-short stature-short fourth metatarsals-intellectual disability syndrome (Orphanet:457395)

HPO phenotypes

82 total (30 of 82 shown, HPO-id order):

HPOTerm
HP:0000007Autosomal recessive inheritance
HP:0000164Abnormality of the dentition
HP:0000252Microcephaly
HP:0000272Malar flattening
HP:0000286Epicanthus
HP:0000316Hypertelorism
HP:0000369Low-set ears
HP:0000470Short neck
HP:0000486Strabismus
HP:0000508Ptosis
HP:0000520Proptosis
HP:0000598Abnormality of the ear
HP:0000729Autistic behavior
HP:0000750Delayed speech and language development
HP:0000766Abnormal sternum morphology
HP:0000926Platyspondyly
HP:0000938Osteopenia
HP:0001156Brachydactyly
HP:0001249Intellectual disability
HP:0001256Mild intellectual disability
HP:0001270Motor delay
HP:0001288Gait disturbance
HP:0001290Generalized hypotonia
HP:0001363Craniosynostosis
HP:0001377Limited elbow extension
HP:0001498Carpal bone hypoplasia
HP:0001643Patent ductus arteriosus
HP:0001653Mitral regurgitation
HP:0001655Patent foramen ovale
HP:0001761Pes cavus

GWAS associations

3 associations (top):

StudyTraitp-value
GCST004029_37Angiotensin-converting enzyme inhibitor intolerance1.000000e-06
GCST008159_47Waist-to-hip ratio adjusted for BMI2.000000e-06
GCST010396_159Gut microbiota (bacterial taxa, hurdle binary method)2.000000e-06

EFO canonical traits (3, from GWAS)

EFO IDTrait name
EFO:0005325response to angiotensin-converting enzyme inhibitor
EFO:0007788BMI-adjusted waist-hip ratio
EFO:0007874gut microbiome measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

18 total (human), top 18 by PubMed support.

ChemicalActions (top 5)PubMed papers
sodium arseniteincreases abundance, increases expression2
beta-lapachonedecreases expression1
manganese chlorideincreases abundance, increases expression1
di-n-butylphosphoric acidaffects expression1
abrineincreases expression1
Resveratrolincreases expression, affects cotreatment1
Arsenicincreases abundance, increases expression1
Atrazineincreases expression1
Benzeneincreases expression1
Benzo(a)pyreneaffects methylation1
Clozapineaffects cotreatment, increases expression1
Cuprizoneaffects cotreatment, increases expression1
Doxorubicindecreases expression1
Leadaffects splicing1
Manganeseincreases abundance, increases expression1
Plant Extractsaffects cotreatment, increases expression1
Valproic Aciddecreases methylation1
Vanadatesincreases expression1

Clinical trials (associated diseases)

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