S100G

Summary

S100G (S100 calcium binding protein G, HGNC:1436) is a protein-coding gene on chromosome Xp22.2, encoding Protein S100-G (P29377).

This gene encodes calbindin D9K, a vitamin D-dependent calcium-binding protein. This cytosolic protein belongs to a family of calcium-binding proteins that includes calmodulin, parvalbumin, troponin C, and S100 protein. In the intestine, the protein is vitamin D-dependent and its expression correlates with calcium transport activity. The protein may increase Ca2+ absorption by buffering Ca2+ in the cytoplasm and increase ATP-dependent Ca2+ transport in duodenal basolateral membrane vesicles.

Source: NCBI Gene 795 — RefSeq curated summary.

At a glance

• GWAS associations: 7
• Clinical variants (ClinVar): 20 total
• MANE Select transcript: NM_004057

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:1436
Approved symbol	S100G
Name	S100 calcium binding protein G
Location	Xp22.2
Locus type	gene with protein product
Status	Approved
Aliases	CABP9K, CABP1
Ensembl gene	ENSG00000169906
Ensembl biotype	protein_coding
OMIM	302020
Entrez	795

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000380200

RefSeq mRNA: 1 — MANE Select: NM_004057 NM_004057

CCDS: CCDS14176

Canonical transcript exons

ENST00000380200 — 3 exons

Exon	Start	End
ENSE00001150725	16650158	16650203
ENSE00001484094	16654405	16654670
ENSE00001484095	16650999	16651141

Expression profiles

Bgee: expression breadth broad, 51 present calls, max score 98.72.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.1525 / max 116.7057, expressed in 6 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
195634	0.1525	6

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
jejunal mucosa	UBERON:0000399	98.72	gold quality
duodenum	UBERON:0002114	95.62	gold quality
jejunum	UBERON:0002115	77.66	gold quality
paraflocculus	UBERON:0005351	66.54	gold quality
middle frontal gyrus	UBERON:0002702	65.93	gold quality
frontal pole	UBERON:0002795	65.90	gold quality
endometrium epithelium	UBERON:0004811	63.83	gold quality
parotid gland	UBERON:0001831	60.32	gold quality
diaphragm	UBERON:0001103	59.54	gold quality
adrenal tissue	UBERON:0018303	57.78	gold quality
calcaneal tendon	UBERON:0003701	57.72	gold quality
oocyte	CL:0000023	56.84	gold quality
left ventricle myocardium	UBERON:0006566	54.54	gold quality
buccal mucosa cell	CL:0002336	52.73	gold quality
colonic epithelium	UBERON:0000397	52.42	silver quality
tendon	UBERON:0000043	51.05	gold quality
Brodmann (1909) area 10	UBERON:0013541	50.18	gold quality
quadriceps femoris	UBERON:0001377	50.11	gold quality
vastus lateralis	UBERON:0001379	49.62	gold quality
metanephric glomerulus	UBERON:0004736	49.61	gold quality
myocardium	UBERON:0002349	49.45	gold quality
Brodmann (1909) area 46	UBERON:0006483	49.30	gold quality
cerebellar vermis	UBERON:0004720	49.25	gold quality
cervix squamous epithelium	UBERON:0006922	49.20	gold quality
hair follicle	UBERON:0002073	49.18	gold quality
olfactory bulb	UBERON:0002264	48.92	gold quality
type B pancreatic cell	CL:0000169	48.83	gold quality
oviduct epithelium	UBERON:0004804	48.65	gold quality
cardiac muscle of right atrium	UBERON:0003379	48.55	gold quality
CA1 field of hippocampus	UBERON:0003881	48.50	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.28

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): CDX2, ESR1, HNF1A, NFKB, PDX1, PGR, SLC24A3, VDR

miRNA regulators (miRDB)

10 targeting S100G, 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-3692-3P	99.98	70.27	2139
HSA-MIR-3934-3P	99.76	65.51	1351
HSA-MIR-1825	99.72	68.11	1089
HSA-MIR-518A-5P	99.70	69.01	2209
HSA-MIR-527	99.70	69.01	2209
HSA-MIR-1275	99.47	67.90	2749
HSA-MIR-4477A	98.83	69.75	2952
HSA-MIR-302F	98.44	69.02	1776
HSA-MIR-4665-5P	97.91	67.69	1536
HSA-MIR-6823-5P	96.26	65.69	919

Literature-anchored findings (GeneRIF, showing 4)

• Cdx-2 is a permissive factor that influences basal CaBP expression in enterocytes and that HNF-1alpha modulates CaBP gene expression during cellular differentiation. (PMID:15217781)
• Parathyroid hormone may inhibit or counteract the increase in CaBP-D9k mRNA caused by 1,25-(OH)2-D3 in Caco-2 cells. (PMID:17712966)
• cultured syncytiotrophoblast cells express calbindin-D9k and calbindin-D28k genes, which are stimulated by calcitriol (PMID:20214988)
• Addition of short-chain fatty acids to cultured Caco-2 cells results in elevation of calbindin-D9k mRNA. (PMID:23132313)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	s100s	ENSDARG00000036773
danio_rerio	s100a10a	ENSDARG00000037425
danio_rerio	s100t	ENSDARG00000055589
mus_musculus	S100g	ENSMUSG00000040808
rattus_norvegicus	S100g	ENSRNOG00000004222

Paralogs (21): CRNN (ENSG00000143536), S100A8 (ENSG00000143546), S100A7 (ENSG00000143556), S100B (ENSG00000160307), S100A1 (ENSG00000160678), S100A11 (ENSG00000163191), S100A9 (ENSG00000163220), S100A12 (ENSG00000163221), S100P (ENSG00000163993), S100Z (ENSG00000171643), S100A7A (ENSG00000184330), S100A3 (ENSG00000188015), S100A16 (ENSG00000188643), SNTN (ENSG00000188817), S100A13 (ENSG00000189171), S100A14 (ENSG00000189334), S100A4 (ENSG00000196154), S100A5 (ENSG00000196420), S100A2 (ENSG00000196754), S100A10 (ENSG00000197747), S100A6 (ENSG00000197956)

Protein

Protein identifiers

Protein S100-G — P29377 (reviewed: P29377)

Alternative names: Calbindin-D9k, S100 calcium-binding protein G, Vitamin D-dependent calcium-binding protein, intestinal

All UniProt accessions (1): P29377

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the S-100 family.

RefSeq proteins (1): NP_004048* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001751	S100/CaBP7/8-like_CS	Conserved_site
IPR002048	EF_hand_dom	Domain
IPR011992	EF-hand-dom_pair	Homologous_superfamily
IPR013787	S100_Ca-bd_sub	Domain
IPR018247	EF_Hand_1_Ca_BS	Binding_site
IPR034325	S-100_dom	Domain

Pfam: PF00036, PF01023

UniProt features (14 total): binding site 7, modified residue 2, domain 2, initiator methionine 1, chain 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P29377-F1	86.91	0.57

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 (7): 69; 26; 31; 58; 60; 62; 64

Post-translational modifications (2): 2, 42

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 206 (showing top): FREAC2_01, MYOGENIN_Q6, GOBP_INTRACELLULAR_PROTEIN_TRANSPORT, NKX25_02, GCANCTGNY_MYOD_Q6, GOBP_PHOTOTRANSDUCTION, GOBP_ESTABLISHMENT_OF_PROTEIN_LOCALIZATION_TO_ORGANELLE, CAGCTG_AP4_Q5, GOBP_NEGATIVE_REGULATION_OF_PROTEIN_LOCALIZATION, GOBP_NUCLEAR_TRANSPORT, MODULE_66, GOBP_NEGATIVE_REGULATION_OF_INTRACELLULAR_PROTEIN_TRANSPORT, CCANNAGRKGGC_UNKNOWN, GOBP_NEGATIVE_REGULATION_OF_TRANSPORT, GOBP_REGULATION_OF_NUCLEOCYTOPLASMIC_TRANSPORT

GO Biological Process (0):

GO Molecular Function (6): vitamin D binding (GO:0005499), calcium ion binding (GO:0005509), transition metal ion binding (GO:0046914), calcium-dependent protein binding (GO:0048306), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (3): cytoplasm (GO:0005737), basolateral plasma membrane (GO:0016323), apical plasma membrane (GO:0016324)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
metal ion binding	2
plasma membrane region	2
steroid binding	1
vitamin binding	1
calcium ion binding	1
protein binding	1
binding	1
cation binding	1
intracellular anatomical structure	1
cellular anatomical structure	1
basal plasma membrane	1
apical part of cell	1

Protein interactions and networks

STRING

1030 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
S100G	CALB1	P05937	969
S100G	TRPV6	Q9H1D0	878
S100G	CABP4	P57796	858
S100G	PVALB	P20472	851
S100G	SDF4	Q9BRK5	792
S100G	CALM1	P02593	774
S100G	CALML3	P27482	770
S100G	CALML6	Q8TD86	769
S100G	CALML4	Q96GE6	769
S100G	CALML5	Q9NZT1	768
S100G	CABP2	Q9NPB3	748
S100G	CALB2	P22676	733
S100G	TRPV5	Q9NQA5	731
S100G	CACNA1F	O60840	699
S100G	S100A2	P29034	688

IntAct

7 interactions, top by confidence:

A	B	Type	Score
NSMF	S100G	psi-mi:“MI:0915”(physical association)	0.560
S100G	NSMF	psi-mi:“MI:0915”(physical association)	0.560
S100G	MYH9	psi-mi:“MI:0407”(direct interaction)	0.440
S100G	SLC8A1	psi-mi:“MI:0407”(direct interaction)	0.440
CEP20	S100G	psi-mi:“MI:0915”(physical association)	0.400

BioGRID (1): S100G (Affinity Capture-Luminescence)

ESM2 similar proteins: A7K6Y8, A7K6Y9, O77791, P02632, P02633, P02634, P02639, P05109, P05942, P06702, P07091, P21457, P23297, P25815, P27004, P27005, P28318, P28782, P29104, P29377, P31227, P31725, P33763, P35467, P50115, P50116, P50117, P56565, P63083, P63084, P79105, P80310, P80363, P80511, P97816, Q14ST5, Q28050, Q2TBI5, Q55G87, Q5R6S5

Diamond homologs: A7K6Y8, A7K6Y9, O77791, P02632, P02633, P02634, P22793, P24480, P29377, P31151, P31725, P50116, P50117, P79105, P80511, P97816, Q14ST5, Q28050, Q503K9, Q6S5I3, Q865V3, Q86SG5, Q8WXG8, O77691, P05964, P06703, P14069, P28318, P30801, P62818, P62819, Q2EN75, P02638, P02639, P04271, P04631, P05942, P06702, P07091, P10462

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
S100G	“up-regulates quantity”	calcium(2+)	relocalization

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	14
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

658 predictions. Top by Δscore:

Variant	Effect	Δscore
X:16651142:G:GG	donor_gain	1.0000
X:16652695:A:AG	acceptor_gain	1.0000
X:16650997:A:G	acceptor_gain	0.9900
X:16651138:CAAAG:C	donor_loss	0.9900
X:16651139:AAAGT:A	donor_loss	0.9900
X:16651140:AA:A	donor_gain	0.9900
X:16651140:AAGTA:A	donor_loss	0.9900
X:16651141:AG:A	donor_loss	0.9900
X:16651143:T:TC	donor_loss	0.9900
X:16651144:AAGTG:A	donor_loss	0.9900
X:16652683:T:G	acceptor_gain	0.9900
X:16652693:A:AG	acceptor_gain	0.9900
X:16652696:A:G	acceptor_gain	0.9900
X:16654395:T:G	acceptor_gain	0.9900
X:16652694:C:G	acceptor_gain	0.9800
X:16654403:AG:A	acceptor_gain	0.9800
X:16654404:GG:G	acceptor_gain	0.9800
X:16654400:AACAG:A	acceptor_gain	0.9700
X:16654403:A:G	acceptor_loss	0.9700
X:16650996:A:AG	acceptor_gain	0.9600
X:16651138:CAAA:C	donor_gain	0.9600
X:16654398:A:AG	acceptor_gain	0.9600
X:16654404:GGGT:G	acceptor_gain	0.9600
X:16654404:GGGTC:G	acceptor_gain	0.9600
X:16650998:G:GG	acceptor_gain	0.9400
X:16651137:TCAAA:T	donor_gain	0.9400
X:16651139:AAA:A	donor_gain	0.9400
X:16654401:ACAG:A	acceptor_gain	0.9400
X:16654403:A:AG	acceptor_gain	0.9400
X:16654404:G:GG	acceptor_gain	0.9400

AlphaMissense

521 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
X:16651086:T:C	L27S	0.988
X:16651046:T:C	F14L	0.984
X:16651048:T:A	F14L	0.984
X:16651048:T:G	F14L	0.984
X:16651101:T:C	L32P	0.972
X:16651058:G:C	A18P	0.964
X:16654463:T:A	V65D	0.964
X:16654477:T:C	F70L	0.957
X:16654479:C:A	F70L	0.957
X:16654479:C:G	F70L	0.957
X:16654478:T:C	F70S	0.955
X:16651110:T:C	L35S	0.954
X:16654441:G:C	D58H	0.950
X:16654442:A:C	D58A	0.950
X:16651047:T:G	F14C	0.944
X:16654439:T:C	L57P	0.943
X:16651086:T:G	L27W	0.940
X:16651047:T:C	F14S	0.927
X:16654442:A:T	D58V	0.926
X:16654443:C:A	D58E	0.925
X:16654443:C:G	D58E	0.925
X:16654475:A:T	E69V	0.919
X:16654465:A:C	S66R	0.918
X:16654467:T:A	S66R	0.918
X:16654467:T:G	S66R	0.918
X:16654427:T:C	L53P	0.916
X:16651059:C:A	A18E	0.914
X:16651055:T:G	Y17D	0.904
X:16654455:T:A	D62E	0.894
X:16654455:T:G	D62E	0.894

dbSNP variants (sampled 300 via entrez): RS1000238498 (X:16649358 T>C), RS1000976761 (X:16652027 C>G), RS1001006198 (X:16652431 C>T), RS1001292677 (X:16651514 T>C), RS1001981952 (X:16654149 C>A), RS1002013075 (X:16654624 T>C), RS1002625713 (X:16653044 T>C), RS1002740635 (X:16653522 A>C), RS1003242729 (X:16649702 G>A), RS1005147530 (X:16651109 T>A,C), RS1005181741 (X:16651598 G>A), RS1006074335 (X:16653624 C>T), RS1006434721 (X:16654049 T>C), RS1006748906 (X:16648180 G>T), RS1007491746 (X:16653198 A>G)

Disease associations

OMIM: gene MIM:302020 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

7 associations (top):

Study	Trait	p-value
GCST003681_15	C-reactive protein levels or triglyceride levels (pleiotropy)	2.000000e-21
GCST007327_93	Smoking status (ever vs never smokers)	9.000000e-10
GCST007576_31	Chronotype	3.000000e-09
GCST008810_83	Smoking initiation (ever regular vs never regular)	3.000000e-08
GCST011096_32	Systemic lupus erythematosus	3.000000e-08
GCST012020_371	Serum metabolite levels	3.000000e-161
GCST90011866_18	Systemic lupus erythematosus	1.000000e-06

EFO canonical traits (5, from GWAS)

EFO ID	Trait name
EFO:0004458	C-reactive protein measurement
EFO:0004530	triglyceride measurement
EFO:0004318	smoking behavior
EFO:0008328	chronotype measurement
EFO:0005670	smoking initiation

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

12 total (human), top 12 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
perfluorooctanoic acid	decreases reaction, increases expression, decreases expression	2
Calcitriol	increases expression, decreases reaction	2
pirinixic acid	affects binding, decreases expression, increases activity	1
perfluorooctane sulfonic acid	decreases expression	1
CGP 52608	affects binding, increases reaction	1
perfluoro-n-nonanoic acid	decreases expression	1
perfluorohexanesulfonic acid	decreases expression	1
trans-10,cis-12-conjugated linoleic acid	increases expression	1
Acetaminophen	decreases expression	1
Ascorbic Acid	affects cotreatment, decreases expression	1
Quercetin	affects cotreatment, decreases expression	1
Palmitic Acid	decreases expression	1

Clinical trials (associated diseases)

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