CIST1

Summary

CIST1 (colon, intestine and stomach enriched 1, HGNC:55823) is a protein-coding gene on chromosome 19p13.11, encoding Protein CIST1 (A0A2R8Y7Y5).

Predicted to be located in membrane.

Source: NCBI Gene 729966 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 5 total
• MANE Select transcript: NM_001396036

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:55823
Approved symbol	CIST1
Name	colon, intestine and stomach enriched 1
Location	19p13.11
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000284797
Ensembl biotype	protein_coding
Entrez	729966

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 2 protein_coding, 1 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000596647, ENST00000600667, ENST00000643046, ENST00000939635

RefSeq mRNA: 1 — MANE Select: NM_001396036 NM_001396036

CCDS: CCDS92568

Canonical transcript exons

ENST00000643046 — 4 exons

Exon	Start	End
ENSE00003819367	18250312	18250472
ENSE00003820203	18250034	18250177
ENSE00003822682	18252064	18252471
ENSE00003823331	18255220	18255362

Expression profiles

Bgee: expression breadth broad, 70 present calls, max score 94.86.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
mucosa of transverse colon	UBERON:0004991	94.86	gold quality
lower esophagus mucosa	UBERON:0035834	85.94	gold quality
duodenum	UBERON:0002114	84.96	gold quality
rectum	UBERON:0001052	83.75	gold quality
esophagus mucosa	UBERON:0002469	76.16	gold quality
transverse colon	UBERON:0001157	73.39	gold quality
body of stomach	UBERON:0001161	68.23	gold quality
small intestine	UBERON:0002108	66.40	gold quality
stomach	UBERON:0000945	66.37	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	66.17	gold quality
small intestine Peyer’s patch	UBERON:0003454	65.19	gold quality
vermiform appendix	UBERON:0001154	64.86	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	64.39	gold quality
mucosa of stomach	UBERON:0001199	63.63	gold quality
gall bladder	UBERON:0002110	62.67	gold quality
intestine	UBERON:0000160	59.20	gold quality
body of pancreas	UBERON:0001150	59.16	gold quality
fundus of stomach	UBERON:0001160	57.80	gold quality
colon	UBERON:0001155	56.50	gold quality
pancreas	UBERON:0001264	56.32	gold quality
colonic epithelium	UBERON:0000397	54.52	gold quality
right uterine tube	UBERON:0001302	53.84	gold quality
tonsil	UBERON:0002372	53.47	gold quality
fallopian tube	UBERON:0003889	50.72	gold quality
esophagus	UBERON:0001043	50.65	gold quality
sural nerve	UBERON:0015488	49.84	silver quality
islet of Langerhans	UBERON:0000006	49.06	gold quality
urinary bladder	UBERON:0001255	47.02	gold quality
metanephros cortex	UBERON:0010533	46.75	gold quality
left testis	UBERON:0004533	46.24	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-GEOD-125970	yes	19.90
E-ANND-3	yes	3.73

Regulation

Is transcription factor: no

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Gm3336	ENSMUSG00000095026
rattus_norvegicus	Cist1	ENSRNOG00000043249

Protein

Protein identifiers

Protein CIST1 — A0A2R8Y7Y5 (reviewed: A0A2R8Y7Y5)

Alternative names: Colon intestine and stomach enriched-protein 1

All UniProt accessions (1): A0A2R8Y7Y5

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

RefSeq proteins (1): NP_001382965* (*=MANE)

Domains & families (InterPro)

UniProt features (9 total): compositionally biased region 3, topological domain 2, signal peptide 1, chain 1, transmembrane region 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A0A2R8Y7Y5-F1	55.47	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 2 (showing top): chr19p13, BUSSLINGER_GASTRIC_ISTHMUS_CELLS

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (1): membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	1

Protein interactions and networks

STRING

14 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CIST1	KXD1	Q9BQD3	230
CIST1	HAVCR1	Q96D42	212
CIST1	PGPEP1	Q9NXJ5	210
CIST1	SECTM1	Q8WVN6	175
CIST1	TIMD4	Q96H15	166
CIST1	LRRC25	Q8N386	166
CIST1	LSM4	Q9Y4Z0	166

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A0A2R8Y7Y5, A1KXC4, A6QLF8, J3KML8, O00592, O35188, O55145, O57604, P06484, P07141, P13838, P14220, P15702, P16150, P18827, P20934, P26260, P34740, P47951, P59647, P78423, P97808, Q08DZ5, Q1ECS6, Q28270, Q28645, Q29RT9, Q3MIW9, Q3TNW5, Q52S86, Q58Y74, Q5RAF8, Q62170, Q64314, Q6MG22, Q6P9X9, Q6UWI2, Q6UXF1, Q86YL7, Q8BHE4

Diamond homologs: A0A2R8Y7Y5, Q1ECS6

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	1
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

624 predictions. Top by Δscore:

Variant	Effect	Δscore
19:18250468:TGGAG:T	acceptor_gain	1.0000
19:18250470:GAG:G	acceptor_gain	1.0000
19:18250473:C:CC	acceptor_gain	1.0000
19:18250473:CTGG:C	acceptor_loss	1.0000
19:18250474:T:A	acceptor_loss	1.0000
19:18252162:C:CC	acceptor_gain	1.0000
19:18255217:TACC:T	donor_loss	1.0000
19:18255219:C:CA	donor_loss	1.0000
19:18250132:ACT:A	donor_gain	0.9900
19:18250133:CTC:C	donor_gain	0.9900
19:18250469:GGAG:G	acceptor_gain	0.9900
19:18250471:AG:A	acceptor_gain	0.9900
19:18252259:T:TA	donor_gain	0.9900
19:18250308:TTA:T	donor_loss	0.9800
19:18250311:C:CT	donor_loss	0.9800
19:18250314:TGGAC:T	donor_gain	0.9800
19:18252157:CGGAA:C	acceptor_gain	0.9800
19:18255218:A:AC	donor_gain	0.9800
19:18255219:C:CC	donor_gain	0.9800
19:18250310:A:AC	donor_gain	0.9700
19:18250311:C:CC	donor_gain	0.9700
19:18250109:T:C	donor_gain	0.9600
19:18250312:C:A	donor_loss	0.9500
19:18252255:ATCAT:A	donor_gain	0.9500
19:18255216:TTACC:T	donor_gain	0.9500
19:18255217:TACCT:T	donor_gain	0.9500
19:18250341:TGG:T	donor_gain	0.9400
19:18252059:CTCA:C	donor_loss	0.9300
19:18252060:TCA:T	donor_loss	0.9300
19:18252061:CA:C	donor_loss	0.9300

AlphaMissense

1515 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:18250413:A:G	C186R	0.990
19:18250386:C:G	G195R	0.961
19:18250386:C:T	G195R	0.961
19:18250385:C:T	G195E	0.960
19:18250336:A:C	F211L	0.957
19:18250336:A:T	F211L	0.957
19:18250338:A:G	F211L	0.957
19:18250397:A:C	L191R	0.910
19:18250391:A:C	L193R	0.906
19:18250411:A:C	C186W	0.904
19:18250391:A:T	L193H	0.901
19:18250151:A:C	F228L	0.894
19:18250151:A:T	F228L	0.894
19:18250153:A:G	F228L	0.894
19:18250406:A:C	L188R	0.891
19:18250418:A:T	V184D	0.885
19:18250403:A:T	V189E	0.884
19:18250412:C:T	C186Y	0.883
19:18250421:A:T	V183E	0.881
19:18250397:A:T	L191H	0.857
19:18250337:A:C	F211C	0.855
19:18250388:A:T	I194N	0.854
19:18250415:A:T	V185E	0.853
19:18250379:A:T	V197E	0.846
19:18250376:A:T	V198D	0.844
19:18250370:G:T	A200D	0.837
19:18250424:A:T	V182E	0.812
19:18250397:A:G	L191P	0.779
19:18250406:A:T	L188Q	0.775
19:18250400:G:T	S190Y	0.764

dbSNP variants (sampled 300 via entrez): RS1000231320 (19:18249768 T>C), RS1000249834 (19:18253561 A>AC,ACAC), RS1001346054 (19:18254198 G>A), RS1001450092 (19:18254228 C>T), RS1001552453 (19:18255317 G>A), RS1001837268 (19:18253786 C>T), RS1001919653 (19:18255151 A>T), RS1004377090 (19:18252592 CTCTCTCTCTCTCTT>C), RS1004986195 (19:18251315 G>A,T), RS1005080970 (19:18251749 C>A,G,T), RS1005195393 (19:18256715 C>G), RS1005638869 (19:18254206 G>A), RS1006503084 (19:18254598 G>T), RS1006666369 (19:18256290 T>C), RS1006738327 (19:18256609 G>A,T)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

Clinical trials (associated diseases)

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