SCGB1C1

Summary

SCGB1C1 (secretoglobin family 1C member 1, HGNC:18394) is a protein-coding gene on chromosome 11p15.5, encoding Secretoglobin family 1C member 1 (Q8TD33).

Predicted to be located in extracellular region.

Source: NCBI Gene 147199 — RefSeq curated summary.

At a glance

• GWAS associations: 5
• Clinical variants (ClinVar): 11 total
• MANE Select transcript: NM_145651

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:18394
Approved symbol	SCGB1C1
Name	secretoglobin family 1C member 1
Location	11p15.5
Locus type	gene with protein product
Status	Approved
Aliases	RYD5
Ensembl gene	ENSG00000188076
Ensembl biotype	protein_coding
OMIM	610176
Entrez	147199

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000342878

RefSeq mRNA: 1 — MANE Select: NM_145651 NM_145651

CCDS: CCDS41581

Canonical transcript exons

ENST00000342878 — 3 exons

Exon	Start	End
ENSE00001386196	194418	194575
ENSE00001601221	193078	193154
ENSE00001702025	193712	193911

Expression profiles

Bgee: expression breadth broad, 99 present calls, max score 79.40.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0025 / max 1.7159, expressed in 1 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
112140	0.0025	1

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
monocyte	CL:0000576	79.40	gold quality
leukocyte	CL:0000738	77.53	gold quality
granulocyte	CL:0000094	62.40	gold quality
body of pancreas	UBERON:0001150	56.31	gold quality
blood	UBERON:0000178	56.03	gold quality
mucosa of stomach	UBERON:0001199	48.15	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	47.46	gold quality
pancreas	UBERON:0001264	46.84	gold quality
vermiform appendix	UBERON:0001154	46.59	gold quality
cerebellar hemisphere	UBERON:0002245	45.08	gold quality
cerebellar cortex	UBERON:0002129	44.89	gold quality
cerebellum	UBERON:0002037	44.72	gold quality
right hemisphere of cerebellum	UBERON:0014890	44.29	gold quality
sural nerve	UBERON:0015488	43.31	gold quality
bone marrow	UBERON:0002371	42.50	gold quality
right lung	UBERON:0002167	41.47	silver quality
bone marrow cell	CL:0002092	39.44	gold quality
tonsil	UBERON:0002372	39.07	silver quality
descending thoracic aorta	UBERON:0002345	38.79	gold quality
superior frontal gyrus	UBERON:0002661	38.17	silver quality
skeletal muscle tissue	UBERON:0001134	37.22	gold quality
colonic epithelium	UBERON:0000397	37.20	gold quality
thoracic mammary gland	UBERON:0005200	36.92	gold quality
ventricular zone	UBERON:0003053	36.48	gold quality
cortical plate	UBERON:0005343	36.47	gold quality
right ovary	UBERON:0002118	36.04	silver quality
omental fat pad	UBERON:0010414	35.87	gold quality
muscle tissue	UBERON:0002385	35.49	silver quality
ganglionic eminence	UBERON:0004023	35.49	gold quality
spleen	UBERON:0002106	34.68	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.77

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

12 targeting SCGB1C1, 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-6851-5P	100.00	65.63	1294
HSA-MIR-889-5P	99.41	68.75	1025
HSA-MIR-6799-5P	99.14	65.72	2093
HSA-MIR-3188	98.58	65.60	878
HSA-MIR-1199-5P	98.44	66.51	829
HSA-MIR-6751-3P	98.44	66.35	835
HSA-MIR-1233-5P	98.19	66.71	1201
HSA-MIR-6778-5P	98.19	66.59	1239
HSA-MIR-644A	96.02	66.52	786
HSA-MIR-3679-5P	94.75	66.46	862
HSA-MIR-1185-5P	94.47	65.95	725
HSA-MIR-553	94.01	65.93	158

Literature-anchored findings (GeneRIF, showing 2)

• Ryd5 single nucleotide polymorphisms and increased risk of nasal polyposis with asthma and allergy (PMID:26204469)
• results suggested that promotor variations in the function of the Secretoglobin 1C1 gene can alter the gene expression biology in nasal polyposis. (PMID:29412801)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Scgb1c1	ENSMUSG00000038801
rattus_norvegicus	Scgb1c1	ENSRNOG00000012847

Paralogs (2): SCGB1A1 (ENSG00000149021), SCGB1C2 (ENSG00000268320)

Protein

Protein identifiers

Secretoglobin family 1C member 1 — Q8TD33 (reviewed: Q8TD33)

Alternative names: Secretoglobin RYD5

All UniProt accessions (1): Q8TD33

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Secreted.

Similarity. Belongs to the secretoglobin family.

RefSeq proteins (1): NP_663626* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR016126	Secretoglobin	Family
IPR035960	Secretoglobin_sf	Homologous_superfamily
IPR043215	Secretoglobin_1C-like	Family

Pfam: PF01099

UniProt features (3 total): signal peptide 1, chain 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8TD33-F1	78.35	0.17

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 9 (showing top): ZWANG_TRANSIENTLY_UP_BY_2ND_EGF_PULSE_ONLY, GSE14415_NATURAL_TREG_VS_FOXP3_KO_NATURAL_TREG_UP, MIR553, GSE10500_ARTHRITIC_SYNOVIAL_FLUID_VS_HEALTHY_MACROPHAGE_UP, HAY_BONE_MARROW_PLATELET, THAKAR_PBMC_INACTIVATED_INFLUENZA_AGE_21_30YO_RESPONDERS_28DY_UP, TRAVAGLINI_LUNG_PLATELET_MEGAKARYOCYTE_CELL, ACEVEDO_LIVER_CANCER_WITH_H3K9ME3_UP, chr11p15

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (1): extracellular region (GO:0005576)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	1

Protein interactions and networks

STRING

408 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SCGB1C1	BPIFB3	P59826	573
SCGB1C1	BPIFB4	P59827	531
SCGB1C1	SCGB3A2	Q96PL1	506
SCGB1C1	SCGB1D1	O95968	447
SCGB1C1	MST1	P26927	416
SCGB1C1	CACNA1B	Q00975	416
SCGB1C1	SCGB3A1	Q96QR1	412
SCGB1C1	TCAF1	Q9Y4C2	412
SCGB1C1	PTPN20	Q4JDL3	410
SCGB1C1	SCGB1D2	O95969	408
SCGB1C1	SCGB1D4	Q6XE38	407
SCGB1C1	BET1L	Q9NYM9	396
SCGB1C1	GPRIN2	O60269	387
SCGB1C1	GNAZ	P19086	379
SCGB1C1	NPY4R2	P0DQD5	378

IntAct

4 interactions, top by confidence:

A	B	Type	Score
BMP2K	SCGB1C1	psi-mi:“MI:0915”(physical association)	0.370
M		psi-mi:“MI:0914”(association)	0.350
SCGB1C1	LAMA5	psi-mi:“MI:0914”(association)	0.350

BioGRID (13): SCGB1C2 (Two-hybrid), LAMA5 (Affinity Capture-MS), EMC7 (Affinity Capture-MS), EMC1 (Affinity Capture-MS), ST3GAL4 (Affinity Capture-MS), SEMA6A (Affinity Capture-MS), FLAD1 (Affinity Capture-MS), FZD2 (Affinity Capture-MS), FZD1 (Affinity Capture-MS), COL14A1 (Affinity Capture-MS), BCHE (Affinity Capture-MS), EXT1 (Affinity Capture-MS), FZD7 (Affinity Capture-MS)

ESM2 similar proteins: A0A1B0GTC6, A0A2U3Y4D7, A0A2Y9HRM2, G5BQH4, G5BWH8, G8F204, P01257, P01261, P02652, P02656, P06759, P0CE37, P0CE39, P0CF78, P0DJD2, P0DJG2, P0DKV2, P0DKV3, P0DKV4, P0DM95, P0DM96, P0DMP9, P0DMR2, P0DMT9, P0DN36, P0DP50, P0DP84, P0DP85, P0DP86, P0DP87, P0DTQ3, P0DTQ5, P0DTR6, P0DTS5, P18656, P18659, P33622, P40148, P41547, P70160

Diamond homologs: P0DMR2, Q05702, Q2VPS3, Q7M742, Q8TD33, P02779, P06913, P11684, P17559, Q06318, Q8MKG2, Q8VD96, Q9TS45, Q65C83

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	7
Likely benign	2
Benign	2

Top pathogenic / likely-pathogenic (0)

SpliceAI

307 predictions. Top by Δscore:

Variant	Effect	Δscore
11:193152:GCC:G	donor_gain	1.0000
11:193155:G:GG	donor_gain	1.0000
11:193901:TC:T	donor_gain	0.9800
11:193154:CGT:C	donor_loss	0.9700
11:193155:G:C	donor_loss	0.9700
11:193156:T:A	donor_loss	0.9700
11:193159:G:GG	donor_gain	0.9700
11:193151:TGCC:T	donor_gain	0.9600
11:193151:TGCCG:T	donor_loss	0.9600
11:193152:GCCG:G	donor_gain	0.9600
11:193153:CCG:C	donor_loss	0.9600
11:193155:G:A	donor_loss	0.9600
11:193156:TGAG:T	donor_loss	0.9600
11:193157:G:GT	donor_loss	0.9600
11:193157:GAGT:G	donor_loss	0.9600
11:193158:A:AC	donor_loss	0.9600
11:193159:G:A	donor_loss	0.9600
11:193687:T:TA	acceptor_gain	0.9600
11:193107:G:T	donor_gain	0.9500
11:193159:G:C	donor_loss	0.9500
11:193708:GCA:G	acceptor_loss	0.9500
11:193709:CAGG:C	acceptor_loss	0.9500
11:193711:G:GT	acceptor_loss	0.9500
11:193153:CC:C	donor_gain	0.9400
11:193158:A:AG	donor_gain	0.9400
11:193692:T:G	acceptor_gain	0.9400
11:193708:GCAG:G	acceptor_loss	0.9400
11:193709:CA:C	acceptor_loss	0.9400
11:193150:CTGCC:C	donor_gain	0.9300
11:193512:C:G	donor_gain	0.9300

AlphaMissense

619 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
11:193857:G:C	K67N	0.975
11:193857:G:T	K67N	0.975
11:193890:G:C	K78N	0.971
11:193890:G:T	K78N	0.971
11:193853:T:A	L66H	0.956
11:193774:G:T	G40W	0.951
11:193841:C:A	A62E	0.944
11:193840:G:C	A62P	0.941
11:193753:T:C	F33L	0.935
11:193755:C:A	F33L	0.935
11:193755:C:G	F33L	0.935
11:193907:T:C	L84P	0.934
11:193874:T:C	L73P	0.927
11:193898:T:C	L81P	0.926
11:193831:G:C	A59P	0.925
11:193855:A:G	K67E	0.921
11:193844:T:G	M63R	0.916
11:193754:T:C	F33S	0.914
11:193853:T:C	L66P	0.910
11:193775:G:T	G40V	0.906
11:193769:T:A	L38Q	0.903
11:193832:C:A	A59D	0.898
11:193757:T:A	L34Q	0.894
11:193757:T:C	L34P	0.891
11:193790:T:A	L45H	0.891
11:193820:T:A	V55D	0.891
11:193836:G:C	K60N	0.889
11:193836:G:T	K60N	0.889
11:193766:T:A	L37Q	0.887
11:193844:T:A	M63K	0.887

dbSNP variants (sampled 300 via entrez): RS1000594896 (11:190153 C>G,T), RS1019391608 (11:193202 A>C,G,T), RS1032023130 (11:190157 C>A), RS1045092984 (11:186424 T>A,C), RS1046928428 (11:194152 A>G), RS1050855070 (11:188301 G>A), RS10660936 (11:194332 C>CA), RS1108819 (11:194331 C>A,G,T), RS111305133 (11:189480 T>A,C,G), RS111413327 (11:186579 G>A,C), RS111613001 (11:194616 A>G,T), RS111707881 (11:191650 T>A,C,G), RS111792566 (11:190523 G>A), RS111881374 (11:189552 G>A,C,T), RS112126401 (11:194639 G>A,T)

Disease associations

OMIM: gene MIM:610176 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

5 associations (top):

Study	Trait	p-value
GCST002186_8	Platelet count	5.000000e-12
GCST004599_13	Mean platelet volume	9.000000e-106
GCST008423_8	Uterine fibroids	1.000000e-20
GCST90002395_42	Mean platelet volume	2.000000e-35
GCST90002402_333	Platelet count	1.000000e-10

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004309	platelet count

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
Benzo(a)pyrene	decreases methylation	1
Folic Acid	decreases expression	1
8-Bromo Cyclic Adenosine Monophosphate	increases expression	1
Copper Sulfate	decreases expression	1

Clinical trials (associated diseases)

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