SCEL

gene
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Also known as FLJ21667MGC22531

Summary

SCEL (sciellin, HGNC:10573) is a protein-coding gene on chromosome 13q22.3, encoding Sciellin (O95171). May function in the assembly or regulation of proteins in the cornified envelope.

The protein encoded by this gene is a precursor to the cornified envelope of terminally differentiated keratinocytes. This protein localizes to the periphery of cells and may function in the assembly or regulation of proteins in the cornified envelope. Transcript variants encoding different isoforms exist. A transcript variant utilizing an alternative polyA signal has been described in the literature, but its full-length nature has not been determined.

Source: NCBI Gene 8796 — RefSeq curated summary.

At a glance

  • GWAS associations: 4
  • Clinical variants (ClinVar): 140 total — 1 likely-pathogenic
  • MANE Select transcript: NM_144777

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:10573
Approved symbolSCEL
Namesciellin
Location13q22.3
Locus typegene with protein product
StatusApproved
AliasesFLJ21667, MGC22531
Ensembl geneENSG00000136155
Ensembl biotypeprotein_coding
OMIM604112
Entrez8796

Gene structure

Transcript identifiers

Ensembl transcripts: 111 — 109 protein_coding, 1 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000349847, ENST00000377246, ENST00000469982, ENST00000471491, ENST00000535157, ENST00000856126, ENST00000856127, ENST00000856128, ENST00000856129, ENST00000856130, ENST00000856131, ENST00000856132, ENST00000856133, ENST00000856134, ENST00000856135, ENST00000856136, ENST00000856137, ENST00000856138, ENST00000856139, ENST00000856140, ENST00000856141, ENST00000856142, ENST00000856143, ENST00000856144, ENST00000856145, ENST00000856146, ENST00000856147, ENST00000856148, ENST00000856149, ENST00000856150, ENST00000856151, ENST00000856152, ENST00000856153, ENST00000856154, ENST00000856155, ENST00000856156, ENST00000856157, ENST00000856158, ENST00000856159, ENST00000856160, ENST00000856161, ENST00000856162, ENST00000856163, ENST00000856164, ENST00000856165, ENST00000856166, ENST00000856167, ENST00000856168, ENST00000856169, ENST00000856170, ENST00000856171, ENST00000856172, ENST00000856173, ENST00000856174, ENST00000856175, ENST00000856176, ENST00000856177, ENST00000856178, ENST00000856179, ENST00000856180, ENST00000856181, ENST00000856182, ENST00000856183, ENST00000856184, ENST00000856185, ENST00000856186, ENST00000856187, ENST00000856188, ENST00000856189, ENST00000965413, ENST00000965414, ENST00000965415, ENST00000965416, ENST00000965417, ENST00000965418, ENST00000965419, ENST00000965420, ENST00000965421, ENST00000965422, ENST00000965423, ENST00000965424, ENST00000965425, ENST00000965426, ENST00000965427, ENST00000965428, ENST00000965429, ENST00000965430, ENST00000965431, ENST00000965432, ENST00000965433, ENST00000965434, ENST00000965435, ENST00000965436, ENST00000965437, ENST00000965438, ENST00000965439, ENST00000965440, ENST00000965441, ENST00000965442, ENST00000965443, ENST00000965444, ENST00000965445, ENST00000965446, ENST00000965447, ENST00000965448, ENST00000965449, ENST00000965450, ENST00000965451, ENST00000965452, ENST00000965453, ENST00000965454

RefSeq mRNA: 3 — MANE Select: NM_144777 NM_001160706, NM_003843, NM_144777

CCDS: CCDS53877, CCDS9458, CCDS9459

Canonical transcript exons

ENST00000349847 — 33 exons

ExonStartEnd
ENSE000005008427756829577568333
ENSE000006846347756768077567748
ENSE000006846377756937177569451
ENSE000008026257755659677556713
ENSE000008026267755980477559863
ENSE000009237567756383177563899
ENSE000009237577757212477572189
ENSE000009237587758914477589224
ENSE000009237597759139577591460
ENSE000009237617759932977599388
ENSE000012350057759351477593573
ENSE000016102707761780377617862
ENSE000016120417761800477618060
ENSE000016395327762794777628009
ENSE000016976587760307677603135
ENSE000017247337763437977634450
ENSE000017315127760265477602713
ENSE000017565507761759977617658
ENSE000017834857764067677640784
ENSE000017839447764270677642808
ENSE000018026377763712077637194
ENSE000018354477753570677535824
ENSE000018819897764425877645263
ENSE000021571277755585777555918
ENSE000035000967760905877609117
ENSE000035436217760805677608115
ENSE000035441007761004777610106
ENSE000035463347759968977599748
ENSE000035836967760206577602124
ENSE000036044997761289177612941
ENSE000036359747759754577597589
ENSE000036657327760435677604415
ENSE000036763097761389377613955

Expression profiles

Bgee: expression breadth ubiquitous, 183 present calls, max score 99.58.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 4.0350 / max 606.2895, expressed in 169 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter IDTPM avgSamples expressed
1355061.8815144
1355091.6863133
1355070.197469
1355080.150659
1355050.119244

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
tongue squamous epitheliumUBERON:000691999.58gold quality
lower esophagus mucosaUBERON:003583499.52gold quality
upper leg skinUBERON:000426299.39gold quality
oral cavityUBERON:000016799.07gold quality
upper arm skinUBERON:000426398.92gold quality
pharyngeal mucosaUBERON:000035598.56gold quality
skin of hipUBERON:000155498.08gold quality
esophagus mucosaUBERON:000246997.98gold quality
skin of abdomenUBERON:000141697.94gold quality
buccal mucosa cellCL:000233697.83gold quality
skin of legUBERON:000151197.73gold quality
esophagus squamous epitheliumUBERON:000692097.57gold quality
zone of skinUBERON:000001497.50gold quality
amniotic fluidUBERON:000017397.49gold quality
squamous epitheliumUBERON:000691496.85gold quality
epithelium of esophagusUBERON:000197696.74gold quality
gingivaUBERON:000182896.24gold quality
penisUBERON:000098995.48gold quality
body of tongueUBERON:001187695.29gold quality
gingival epitheliumUBERON:000194995.27gold quality
right lungUBERON:000216795.26gold quality
mammalian vulvaUBERON:000099795.22gold quality
cervix squamous epitheliumUBERON:000692295.12gold quality
cervix epitheliumUBERON:000480194.26gold quality
upper lobe of left lungUBERON:000895293.22gold quality
upper lobe of lungUBERON:000894892.95gold quality
palpebral conjunctivaUBERON:000181290.95gold quality
tongueUBERON:000172388.11gold quality
lungUBERON:000204886.95gold quality
vaginaUBERON:000099686.09gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 3.

ExperimentMarker?Max mean expression
E-MTAB-7249yes690.44
E-GEOD-130148yes9.58
E-ANND-3yes9.09
E-CURD-10no64.17

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

66 targeting SCEL, 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-126-5P100.0072.713180
HSA-MIR-30A-5P100.0076.313233
HSA-MIR-30B-5P100.0076.293248
HSA-MIR-30C-5P100.0076.293248
HSA-MIR-30D-5P100.0076.323233
HSA-MIR-30E-5P100.0076.323242
HSA-MIR-5011-5P100.0083.465820
HSA-MIR-4795-3P100.0074.624024
HSA-MIR-6867-5P100.0082.213464
HSA-MIR-520D-5P99.9873.344883
HSA-MIR-524-5P99.9873.434882
HSA-MIR-477599.9875.006394
HSA-MIR-568899.9673.234504
HSA-MIR-495-3P99.9672.814197
HSA-MIR-1250-3P99.9670.044038
HSA-MIR-3682-5P99.9367.971163
HSA-MIR-7-1-3P99.9171.534384
HSA-MIR-7-2-3P99.9171.404394
HSA-MIR-627-3P99.9071.423316
HSA-MIR-380-3P99.8970.181978
HSA-MIR-153-5P99.8973.866317
HSA-MIR-806299.8868.43995
HSA-MIR-391999.8769.452489
HSA-MIR-5582-3P99.8672.484221
HSA-MIR-202-3P99.8471.411290
HSA-MIR-449599.8272.083080
HSA-MIR-313399.8170.923506
HSA-MIR-4760-5P99.8069.881619
HSA-MIR-57799.7869.132479
HSA-MIR-451799.7669.191867

Literature-anchored findings (GeneRIF, showing 8)

  • VDUP1 and sciellin were more highly expressed in keratinocytes undergoing differentiation and colocalization of the proteins could be demonstrated (PMID:14632196)
  • Single nucleotide polymorphisms were detected in both matching tumor and normal esophageal tissues but no disease-associated mutations suggesting that SCEL is not a major factor in esophageal squamous cell carcinogenesis. (PMID:15274303)
  • Sciellin, SPRR3, and periplakin transcripts were all upregulated (4.67-, 4.95-, 2.77-fold, respectively) by prolonged exposure to cyclic strain (24-72 h), but not at earlier time points. (PMID:19211270)
  • These results demonstrate that SCEL is a mesenchymal-to-epithelial transition inducer dynamically regulated through the metastasis process (PMID:27013588)
  • Down-regulation of long non-coding RNA HOTAIR promotes angiogenesis via regulating miR-126/SCEL pathways in burn wound healing. (PMID:31974341)
  • Clinical significance and diagnostic value of QPCT, SCEL and TNFRSF12A in papillary thyroid cancer. (PMID:37060824)
  • CBX8 promotes lung adenocarcinoma growth and metastasis through transcriptional repression of CDKN2C and SCEL. (PMID:37733753)
  • Sciellin promotes the development and progression of thyroid cancer through the JAK2/STAT3 signaling pathway. (PMID:38411346)

Cross-species orthologs

2 orthologs

OrganismSymbolGene ID
mus_musculusScelENSMUSG00000022123
rattus_norvegicusScelENSRNOG00000024237

Paralogs (1): ZNF185 (ENSG00000147394)

Protein

Protein identifiers

SciellinO95171 (reviewed: O95171)

All UniProt accessions (2): O95171, F2Z2X8

UniProt curated annotations — full annotation on UniProt →

Function. May function in the assembly or regulation of proteins in the cornified envelope. The LIM domain may be involved in homotypic or heterotypic associations and may function to localize sciellin to the cornified envelope.

Subcellular location. Cytoplasm. Membrane.

Tissue specificity. Highly expressed in esophagus. It is also expressed in keratinocytes, amniotic tissue, foreskin stratum spinosum and stratum granulosum, hair follicle and nail.

Isoforms (3)

UniProt IDNamesCanonical?
O95171-11yes
O95171-22
O95171-33

RefSeq proteins (3): NP_001154178, NP_003834, NP_659001* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001781Znf_LIMDomain
IPR052621Cell_Prolif/Cornif_RegulFamily

UniProt features (41 total): repeat 16, sequence conflict 6, region of interest 4, compositionally biased region 4, modified residue 3, splice variant 3, sequence variant 3, chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-O95171-F145.480.02

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 (3): 83, 289, 389

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 153 (showing top): AP1_01, GOBP_EMBRYO_DEVELOPMENT_ENDING_IN_BIRTH_OR_EGG_HATCHING, GOBP_EPITHELIUM_DEVELOPMENT, GOBP_REGULATION_OF_WNT_SIGNALING_PATHWAY, ONDER_CDH1_TARGETS_3_DN, GOBP_EPIDERMAL_CELL_DIFFERENTIATION, FONTAINE_PAPILLARY_THYROID_CARCINOMA_UP, GOBP_CANONICAL_WNT_SIGNALING_PATHWAY, TGANTCA_AP1_C, GOBP_EPIDERMIS_DEVELOPMENT, GOBP_RESPONSE_TO_ABIOTIC_STIMULUS, GOBP_POSITIVE_REGULATION_OF_CANONICAL_WNT_SIGNALING_PATHWAY, AIGNER_ZEB1_TARGETS, GOBP_EMBRYO_DEVELOPMENT, AML1_01

GO Biological Process (5): epidermis development (GO:0008544), response to mechanical stimulus (GO:0009612), embryo development ending in birth or egg hatching (GO:0009792), keratinocyte differentiation (GO:0030216), positive regulation of canonical Wnt signaling pathway (GO:0090263)

GO Molecular Function (2): metal ion binding (GO:0046872), protein binding (GO:0005515)

GO Cellular Component (5): cornified envelope (GO:0001533), cytoplasm (GO:0005737), perinuclear region of cytoplasm (GO:0048471), extracellular exosome (GO:0070062), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure3
tissue development1
response to external stimulus1
response to abiotic stimulus1
embryo development1
epidermal cell differentiation1
skin development1
positive regulation of Wnt signaling pathway1
canonical Wnt signaling pathway1
regulation of canonical Wnt signaling pathway1
cation binding1
binding1
plasma membrane1
intracellular anatomical structure1
cytoplasm1
extracellular vesicle1

Protein interactions and networks

STRING

1332 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
SCELSULF1Q8IWU6752
SCELYIPF3Q9GZM5711
SCELSYNPOQ8N3V7705
SCELCYP26A1O43174693
SCELACTN4O43707637
SCELNPHS1O60500598
SCELSPRR2AP35326559
SCELPOU4F2Q12837547
SCELLCE3DQ9BYE3543
SCELPODXLO00592513
SCELWT1P19544511
SCELLHX9Q9NQ69503
SCELTJP1Q07157502
SCELPAX2Q02962492
SCELTGM3Q08188487

IntAct

55 interactions, top by confidence:

ABTypeScore
FXR2SCELpsi-mi:“MI:0915”(physical association)0.670
SCELGOLGA2psi-mi:“MI:0915”(physical association)0.670
SCELNMIpsi-mi:“MI:0915”(physical association)0.670
SCELFXR2psi-mi:“MI:0915”(physical association)0.670
NMISCELpsi-mi:“MI:0915”(physical association)0.670
SCELMTUS2psi-mi:“MI:0915”(physical association)0.560
SCELKIFC3psi-mi:“MI:0915”(physical association)0.560
SCELTSGA10psi-mi:“MI:0915”(physical association)0.560
MTUS2SCELpsi-mi:“MI:0915”(physical association)0.560
KIFC3SCELpsi-mi:“MI:0915”(physical association)0.560
TBC1D22BA2ML1psi-mi:“MI:0914”(association)0.530
FRMD1A2ML1psi-mi:“MI:0914”(association)0.530
SCELLRRK2psi-mi:“MI:0407”(direct interaction)0.440
SCELDAPK1psi-mi:“MI:0407”(direct interaction)0.440
ENGSCELpsi-mi:“MI:0407”(direct interaction)0.440
SCELpsi-mi:“MI:0407”(direct interaction)0.440

BioGRID (43): SCEL (Two-hybrid), SCEL (Two-hybrid), NMI (Two-hybrid), FXR2 (Two-hybrid), MTUS2 (Two-hybrid), TSGA10 (Two-hybrid), SCEL (Reconstituted Complex), SCEL (Two-hybrid), NMI (Two-hybrid), SCEL (Two-hybrid), SCEL (Proximity Label-MS), SCEL (Affinity Capture-MS), RAB11B (Affinity Capture-MS), SCEL (Reconstituted Complex), SCEL (Reconstituted Complex)

ESM2 similar proteins: A0JPP4, A1KXM5, A1YGK6, A2T7F2, A4FU69, A6NE01, A6X8Z9, E9Q0C6, E9Q5F9, E9Q7D5, F6XZJ7, O60057, O95171, P88825, Q03661, Q2T9M9, Q2YDJ5, Q32MG2, Q3URU2, Q3V0C1, Q53TS8, Q5BI31, Q5R7U0, Q5SRN2, Q66H38, Q6AXV6, Q6AYN3, Q70KF4, Q710D7, Q80Y39, Q810T2, Q8BUY8, Q8K4E0, Q8N3K9, Q8NEV8, Q8TC56, Q8TCU4, Q95J40, Q95JY5, Q95K27

Diamond homologs: O15231, O95171, Q62394, Q9EQG3, Q3KQW7, Q3UH68, Q9UPQ0, B9G8P1, F4HZF0, O81635, P26932, P37397, P37803, P51911, P52735, Q08091, Q08092, Q08093, Q08094, Q08290, Q15052, Q15417, Q24799, Q2HJ38, Q32L92, Q3SYU6, Q54TK8, Q55E26, Q55GV9, Q5RFN6, Q5XXR3, Q60992, Q7YRL2, Q8K4I3, Q8WWI1, Q99439, Q9DAW9, Q9GK38, Q921G6, Q9Y2L9

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic1
Uncertain significance100
Likely benign4
Benign0

Top pathogenic / likely-pathogenic (1)

Variant IDHGVSClassification
982220NM_144777.3(SCEL):c.175G>A (p.Gly59Ser)Likely pathogenic

SpliceAI

4486 predictions. Top by Δscore:

VariantEffectΔscore
13:77556595:GA:Gacceptor_gain1.0000
13:77556709:GAAAA:Gdonor_gain1.0000
13:77556714:G:GGdonor_gain1.0000
13:77559802:A:AGacceptor_gain1.0000
13:77559803:G:GGacceptor_gain1.0000
13:77563810:T:TAacceptor_gain1.0000
13:77563819:T:Gacceptor_gain1.0000
13:77569368:CAGG:Cacceptor_loss1.0000
13:77569369:A:AGacceptor_gain1.0000
13:77569369:AGGCA:Aacceptor_loss1.0000
13:77569370:G:GGacceptor_gain1.0000
13:77569447:AAGAG:Adonor_loss1.0000
13:77569448:AGAGG:Adonor_loss1.0000
13:77569449:GAG:Gdonor_gain1.0000
13:77569450:AGGTA:Adonor_loss1.0000
13:77569451:GG:Gdonor_loss1.0000
13:77569452:GTAG:Gdonor_loss1.0000
13:77569453:T:Adonor_loss1.0000
13:77589140:AAAG:Aacceptor_gain1.0000
13:77597541:A:AGacceptor_gain1.0000
13:77597542:A:Gacceptor_gain1.0000
13:77597543:A:Gacceptor_gain1.0000
13:77597544:G:GAacceptor_gain1.0000
13:77597544:GT:Gacceptor_gain1.0000
13:77597588:AGGT:Adonor_loss1.0000
13:77597590:GTA:Gdonor_loss1.0000
13:77599687:A:AGacceptor_gain1.0000
13:77599688:G:GGacceptor_gain1.0000
13:77599688:GA:Gacceptor_gain1.0000
13:77599747:GG:Gdonor_gain1.0000

AlphaMissense

4624 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
13:77640698:T:AC621S0.999
13:77640698:T:CC621R0.999
13:77640699:G:CC621S0.999
13:77640700:C:GC621W0.998
13:77642706:T:AC650S0.997
13:77642706:T:CC650R0.997
13:77642707:G:CC650S0.997
13:77640699:G:AC621Y0.996
13:77640707:T:AC624S0.996
13:77640708:G:CC624S0.996
13:77640707:T:CC624R0.995
13:77640776:T:CC647R0.995
13:77640778:C:GC647W0.995
13:77640708:G:AC624Y0.994
13:77640709:C:GC624W0.994
13:77640780:T:CF648S0.994
13:77642708:T:GC650W0.994
13:77642715:T:AC653S0.994
13:77642716:G:CC653S0.994
13:77642792:C:GC678W0.994
13:77640699:G:TC621F0.993
13:77640766:C:GC643W0.993
13:77640769:T:AH644Q0.993
13:77640769:T:GH644Q0.993
13:77642715:T:CC653R0.993
13:77642790:T:AC678S0.993
13:77642790:T:CC678R0.993
13:77642791:G:CC678S0.993
13:77572131:T:AW163R0.992
13:77572131:T:CW163R0.992

dbSNP variants (sampled 300 via entrez): RS1000035019 (13:77594938 G>A), RS1000039649 (13:77550776 T>A), RS1000045521 (13:77558129 A>G), RS1000064980 (13:77537038 T>C), RS1000136695 (13:77549362 T>A,C), RS1000145391 (13:77628520 A>G), RS1000147775 (13:77640747 A>G), RS1000225491 (13:77595856 T>C), RS1000227872 (13:77623386 C>T), RS1000243566 (13:77562909 G>A), RS1000321449 (13:77576308 C>G), RS1000336954 (13:77569787 C>A), RS1000339685 (13:77616291 A>G,T), RS1000429972 (13:77602529 A>G,T), RS1000454688 (13:77557059 C>G,T)

Disease associations

OMIM: gene MIM:604112 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (1): Moyamoya angiopathy (Orphanet:477768)

HPO phenotypes

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

GWAS associations

4 associations (top):

StudyTraitp-value
GCST004412_10Craniofacial microsomia8.000000e-06
GCST007565_111Morning person4.000000e-19
GCST007576_398Chronotype4.000000e-19
GCST008477_17Emphysema annual change measurement in smokers (adjusted lung density)6.000000e-06

EFO canonical traits (2, from GWAS)

EFO IDTrait name
EFO:0008328chronotype measurement
EFO:0007626emphysema imaging measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
sodium arsenitedecreases expression, increases expression3
Particulate Matterincreases expression, decreases expression, increases abundance3
Benzo(a)pyrenedecreases expression, decreases methylation, increases methylation2
Estradiolaffects cotreatment, decreases expression2
Tobacco Smoke Pollutionaffects expression, increases expression2
aristolochic acid Idecreases expression1
urushiolincreases expression1
bisphenol Aincreases expression1
pyrogallol 1,3-dimethyl etheraffects cotreatment, decreases expression, affects localization1
ethyl-p-hydroxybenzoateincreases expression1
beta-lapachoneincreases expression1
cylindrospermopsinincreases expression1
CGP 52608affects binding, increases reaction1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression1
dorsomorphinaffects cotreatment, increases expression1
NSC 689534affects binding, increases expression1
Zoledronic Aciddecreases expression1
Air Pollutantsdecreases expression, increases abundance1
Vehicle Emissionsincreases abundance, increases expression1
Cadmiumincreases expression1
Calcitrioldecreases expression1
Copperaffects binding, increases expression1
Dexamethasoneincreases expression1
Diurondecreases expression1
Furaldehydeaffects cotreatment, decreases expression, affects localization, increases expression1
Phenylmercuric Acetateincreases expression, affects cotreatment1
Smokedecreases expression1
Sodium Chloridedecreases expression, affects localization, increases expression, affects cotreatment1
Tretinoinincreases expression1
Valproic Acidincreases expression1

Clinical trials (associated diseases)

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

  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): craniofacial microsomia