CEACAM19

Summary

CEACAM19 (CEA cell adhesion molecule 19, HGNC:31951) is a protein-coding gene on chromosome 19q13.31, encoding Cell adhesion molecule CEACAM19 (Q7Z692).

Predicted to be involved in heterophilic cell-cell adhesion and homophilic cell-cell adhesion. Predicted to be located in membrane. Predicted to be active in plasma membrane.

Source: NCBI Gene 56971 — automated summary from GO annotations (Alliance of Genome Resources).

At a glance

• GWAS associations: 4
• Clinical variants (ClinVar): 38 total — 1 pathogenic
• GTEx eGene: eQTL in 47 tissues, sQTL in 3 (q < 0.05)
• Constraint (gnomAD): pLI 0.00 (LoF-tolerant), LOEUF 1.50 (unconstrained)
• MANE Select transcript: NM_001127893

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:31951
Approved symbol	CEACAM19
Name	CEA cell adhesion molecule 19
Location	19q13.31
Locus type	gene with protein product
Status	Approved
Aliases	CEAL1
Ensembl gene	ENSG00000186567
Ensembl biotype	protein_coding
OMIM	606691
Entrez	56971

Gene structure

Transcript identifiers

Ensembl transcripts: 11 — 9 protein_coding, 1 retained_intron, 1 protein_coding_CDS_not_defined

MANE Select: ENST00000358777

Transcript support level (Ensembl TSL; 1 = fully mRNA-supported): TSL 1: 2, TSL 2: 4, TSL 5: 3

ENST00000358777, ENST00000403660, ENST00000459648, ENST00000480278, ENST00000591979, ENST00000592789, ENST00000618372, ENST00000619799, ENST00000622237, ENST00000911248, ENST00001143192

RefSeq mRNA: 3 — MANE Select: NM_001127893 NM_001127893, NM_001389722, NM_020219

CCDS: CCDS12641, CCDS46108

Canonical transcript exons

ENST00000358777 — 8 exons

Exon	Start	End
ENSE00001404578	44671482	44671986
ENSE00001407788	44672596	44672964
ENSE00001826287	44683437	44684355
ENSE00003465574	44681227	44681312
ENSE00003638981	44676271	44676421
ENSE00003657264	44682567	44682620
ENSE00003668088	44678853	44678936
ENSE00003678292	44680288	44680334

Expression profiles

Bgee: expression breadth ubiquitous, 160 present calls, max score 91.31.

Highest expression (Bgee): apex of heart, uterine tube, metanephros cortex, tibial nerve, gastrocnemius.

Genetic regulation across tissues (GTEx eQTL / sQTL)

CEACAM19 is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 47 tissues and its splicing (sQTL) in 3 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.

showing 20 of 50 significant tissue × QTL associations:

Tissue	QTL	q-value	Slope	Lead variant
Thyroid	eqtl	5.3e-57	-0.70	19:44662645:A:C
Cells Cultured fibroblasts	eqtl	2.4e-55	-0.73	19:44662645:A:C
Colon Transverse	eqtl	1.3e-31	-0.73	19:44662645:A:C
Muscle Skeletal	eqtl	3.8e-26	+0.46	19:44641449:G:C
Heart Left Ventricle	eqtl	6.6e-26	-0.68	19:44591944:C:G
Pancreas	eqtl	1.7e-24	-0.82	19:44662645:A:C
Adipose Visceral Omentum	eqtl	1.8e-24	-0.50	19:44662645:A:C
Artery Tibial	eqtl	1.5e-23	-0.48	19:44662645:A:C
Nerve Tibial	eqtl	1.9e-23	+0.65	19:44642317:C:T
Pituitary	eqtl	2.1e-22	-0.74	19:44662645:A:C
Artery Aorta	eqtl	1.1e-21	-0.56	19:44662645:A:C
Prostate	eqtl	3.5e-20	-0.59	19:44662645:A:C
Colon Sigmoid	eqtl	5.4e-18	-0.48	19:44662645:A:C
Brain Frontal Cortex BA9	eqtl	7.8e-18	-0.69	19:44662645:A:C
Esophagus Muscularis	eqtl	5.0e-17	-0.42	19:44662645:A:C
Stomach	eqtl	1.2e-16	-0.61	19:44662645:A:C
Brain Nucleus accumbens basal ganglia	eqtl	1.4e-16	-0.57	19:44662645:A:C
Heart Atrial Appendage	eqtl	7.4e-16	-0.51	19:44662645:A:C
Brain Hypothalamus	eqtl	8.6e-16	-0.59	19:44662645:A:C
Adipose Subcutaneous	eqtl	1.7e-15	-0.43	19:44662645:A:C

Top tissues by expression

showing 100 of 254 tissues by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
apex of heart	UBERON:0002098	91.31	gold quality
right uterine tube	UBERON:0001302	89.01	gold quality
metanephros cortex	UBERON:0010533	87.72	gold quality
tibial nerve	UBERON:0001323	87.18	gold quality
gastrocnemius	UBERON:0001388	86.61	gold quality
muscle of leg	UBERON:0001383	85.54	gold quality
body of pancreas	UBERON:0001150	85.15	gold quality
hindlimb stylopod muscle	UBERON:0004252	84.56	gold quality
right lobe of liver	UBERON:0001114	84.27	gold quality
skin of leg	UBERON:0001511	83.98	gold quality
heart left ventricle	UBERON:0002084	83.74	gold quality
adenohypophysis	UBERON:0002196	83.17	gold quality
cardiac ventricle	UBERON:0002082	83.14	gold quality
stromal cell of endometrium	CL:0002255	82.70	gold quality
skin of abdomen	UBERON:0001416	82.66	gold quality
sural nerve	UBERON:0015488	82.53	gold quality
upper lobe of left lung	UBERON:0008952	82.42	gold quality
left uterine tube	UBERON:0001303	82.11	gold quality
lower esophagus muscularis layer	UBERON:0035833	81.94	gold quality
lower esophagus	UBERON:0013473	81.90	gold quality
popliteal artery	UBERON:0002250	81.71	gold quality
tibial artery	UBERON:0007610	81.71	gold quality
left lobe of thyroid gland	UBERON:0001120	81.66	gold quality
ectocervix	UBERON:0012249	81.62	gold quality
cerebellar hemisphere	UBERON:0002245	81.53	gold quality
right adrenal gland	UBERON:0001233	81.50	gold quality
mucosa of stomach	UBERON:0001199	81.48	gold quality
right hemisphere of cerebellum	UBERON:0014890	81.42	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	81.41	gold quality
right coronary artery	UBERON:0001625	81.36	gold quality
cerebellar cortex	UBERON:0002129	81.34	gold quality
left ovary	UBERON:0002119	81.21	gold quality
pituitary gland	UBERON:0000007	81.19	gold quality
zone of skin	UBERON:0000014	81.10	gold quality
pancreas	UBERON:0001264	80.98	gold quality
right ovary	UBERON:0002118	80.93	gold quality
right adrenal gland cortex	UBERON:0035827	80.86	gold quality
minor salivary gland	UBERON:0001830	80.79	gold quality
left testis	UBERON:0004533	80.76	gold quality
left adrenal gland cortex	UBERON:0035825	80.76	gold quality
aorta	UBERON:0000947	80.36	gold quality
right lobe of thyroid gland	UBERON:0001119	80.35	gold quality
body of stomach	UBERON:0001161	80.32	gold quality
body of uterus	UBERON:0009853	80.25	gold quality
thyroid gland	UBERON:0002046	80.19	gold quality
lower esophagus mucosa	UBERON:0035834	80.15	gold quality
right testis	UBERON:0004534	80.08	gold quality
transverse colon	UBERON:0001157	79.98	gold quality
left adrenal gland	UBERON:0001234	79.94	gold quality
cerebellum	UBERON:0002037	79.94	gold quality
muscle layer of sigmoid colon	UBERON:0035805	79.72	gold quality
heart	UBERON:0000948	79.62	gold quality
mouth mucosa	UBERON:0003729	79.59	gold quality
adrenal cortex	UBERON:0001235	79.50	gold quality
right lung	UBERON:0002167	79.48	gold quality
endocervix	UBERON:0000458	79.11	gold quality
upper lobe of lung	UBERON:0008948	79.08	gold quality
esophagus	UBERON:0001043	78.98	gold quality
ascending aorta	UBERON:0001496	78.93	gold quality
cardiac muscle of right atrium	UBERON:0003379	78.86	gold quality
thoracic aorta	UBERON:0001515	78.81	gold quality
cortical plate	UBERON:0005343	78.72	gold quality
vagina	UBERON:0000996	78.68	gold quality
mucosa of transverse colon	UBERON:0004991	78.65	gold quality
pancreatic ductal cell	CL:0002079	78.55	silver quality
right atrium auricular region	UBERON:0006631	78.49	gold quality
left coronary artery	UBERON:0001626	78.41	gold quality
left ventricle myocardium	UBERON:0006566	78.30	gold quality
cardiac atrium	UBERON:0002081	78.17	gold quality
adrenal gland	UBERON:0002369	78.08	gold quality
coronary artery	UBERON:0001621	78.02	gold quality
metanephros	UBERON:0000081	78.01	gold quality
testis	UBERON:0000473	77.86	gold quality
right frontal lobe	UBERON:0002810	77.80	gold quality
prostate gland	UBERON:0002367	77.66	gold quality
islet of Langerhans	UBERON:0000006	77.58	gold quality
cortex of kidney	UBERON:0001225	77.57	gold quality
uterine cervix	UBERON:0000002	77.52	gold quality
ileal mucosa	UBERON:0000331	77.51	silver quality
small intestine Peyer’s patch	UBERON:0003454	77.44	gold quality
saliva-secreting gland	UBERON:0001044	77.39	gold quality
descending thoracic aorta	UBERON:0002345	77.39	gold quality
stomach	UBERON:0000945	77.22	gold quality
esophagus mucosa	UBERON:0002469	77.11	gold quality
ovary	UBERON:0000992	77.02	gold quality
Brodmann (1909) area 9	UBERON:0013540	76.75	gold quality
omental fat pad	UBERON:0010414	76.73	gold quality
peritoneum	UBERON:0002358	76.69	gold quality
tibialis anterior	UBERON:0001385	76.66	silver quality
anterior cingulate cortex	UBERON:0009835	76.64	gold quality
liver	UBERON:0002107	76.28	gold quality
colon	UBERON:0001155	76.12	gold quality
small intestine	UBERON:0002108	75.69	gold quality
granulocyte	CL:0000094	75.61	gold quality
adipose tissue of abdominal region	UBERON:0007808	75.54	gold quality
hypothalamus	UBERON:0001898	75.52	gold quality
large intestine	UBERON:0000059	75.51	gold quality
intestine	UBERON:0000160	75.50	gold quality
nucleus accumbens	UBERON:0001882	75.43	gold quality
fundus of stomach	UBERON:0001160	75.22	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.13
E-MTAB-6386	no	21.69

HPA expression

RNA tissue specificity: Low tissue specificity

showing 60 of 70 HPA tissues / cells by nTPM:

Tissue / cell	Axis	nTPM
Skeletal muscle	tissue	13.1
Skin 1	tissue	10.2
Postcentral gyrus	tissue	9.7
Choroid plexus	tissue	8.5
Vagina	tissue	8.2
Hippocampus	tissue	7.8
Pituitary gland	tissue	6.8
Nucleus accumbens	tissue	6.2
Locus coeruleus	tissue	5.2
Fallopian tube	tissue	4.0
Pancreas	tissue	3.6
Rectum	tissue	3.3
Liver	tissue	3.3
Testis	tissue	3.2
Heart muscle	tissue	3.2
Tongue	tissue	3.2
Small intestine	tissue	3.1
Prostate	tissue	3.1
Seminal vesicle	tissue	2.9
Smooth muscle	tissue	2.9
Endometrium 1	tissue	2.8
Duodenum	tissue	2.8
Adrenal gland	tissue	2.8
Lung	tissue	2.7
Colon	tissue	2.6
Breast	tissue	2.5
Ovary	tissue	2.5
Salivary gland	tissue	2.4
Retina	tissue	2.2
Esophagus	tissue	2.1
Spleen	tissue	2.1
Gallbladder	tissue	2.1
Stomach 1	tissue	2.0
Placenta	tissue	2.0
Thyroid gland	tissue	2.0
Tonsil	tissue	2.0
Kidney	tissue	1.9
Cervix	tissue	1.8
Adipose tissue	tissue	1.7
Epididymis	tissue	1.7
Bone marrow	tissue	1.6
Hippocampal formation	tissue	1.5
Parathyroid gland	tissue	1.4
Urinary bladder	tissue	1.0
Thymus	tissue	0.9
Appendix	tissue	0.9
Lymph node	tissue	0.8
Cerebral cortex	tissue	0.6
Somatosensory cortex	tissue	0.6
Occipital cortex	tissue	0.6
Entorhinal cortex	tissue	0.5
Temporal cortex	tissue	0.5
Motor cortex	tissue	0.4
Putamen	tissue	0.4
Retrosplenial and cingulate cortex	tissue	0.4
Retrosplenial cortex	tissue	0.4
Prefrontal cortex	tissue	0.3
Pons	tissue	0.3
Amygdala	tissue	0.3
Insular cortex	tissue	0.3

Brain sub-regions (HPA Brain Atlas): detected in 186; highest nTPM — Precentral gyrus (11.6), Flocculonodular lobe (11.3), Parietal operculum (10.6), Somatomor cortex, precentral gyrus (white matter) (10.6), Vermis (10.3).

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

Targeting CEACAM19 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific).

showing 30 of 37 miRNAs:

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-4731-5P	99.89	67.23	2537
HSA-MIR-137-3P	99.87	74.74	2401
HSA-MIR-6739-5P	99.80	67.87	2806
HSA-MIR-6733-5P	99.74	67.94	2759
HSA-MIR-5004-5P	99.68	66.63	1294
HSA-MIR-4516	99.61	67.78	3390
HSA-MIR-1224-5P	99.48	65.59	803
HSA-MIR-1275	99.47	67.90	2749
HSA-MIR-4316	99.37	65.75	1360
HSA-MIR-661	99.09	65.94	2062
HSA-MIR-4651	99.06	67.57	2002
HSA-MIR-153-3P	98.96	72.51	1644
HSA-MIR-608	98.93	67.83	2013
HSA-MIR-6829-5P	98.86	65.12	1480
HSA-MIR-5008-5P	98.42	65.87	1019
HSA-MIR-4717-5P	98.19	67.97	894
HSA-MIR-6801-3P	98.04	64.64	805
HSA-MIR-6810-3P	97.96	64.57	1023
HSA-MIR-6819-5P	97.96	66.59	1071
HSA-MIR-450A-2-3P	97.91	67.56	1459
HSA-MIR-4665-5P	97.91	67.69	1536
HSA-MIR-676-3P	97.86	65.70	668
HSA-MIR-4799-3P	97.78	65.97	893
HSA-MIR-6737-5P	97.75	66.54	1044
HSA-MIR-6812-5P	97.56	65.39	1059
HSA-MIR-4720-5P	97.46	65.67	893
HSA-MIR-5588-5P	97.46	65.70	913
HSA-MIR-2467-5P	97.36	67.71	991
HSA-MIR-6131	97.22	66.72	960
HSA-MIR-10398-5P	97.12	64.94	1051

Functional genomics

gnomAD constraint: pLI 5.97e-13, LOEUF 1.5, missense Z 0.38 — population loss-of-function intolerance (pLI ≥ 0.9 = LoF-intolerant; lower LOEUF = more constrained). gnomAD

Regional missense constraint (gnomAD RMC): no regional variation along ENST00000358777 — one region, missense o/e 0.91.

Literature-anchored findings (GeneRIF, showing 4)

• Our results suggest that CEACAM19 mRNA expression represents a promising, novel and clinically useful tissue biomarker for breast cancer management. (PMID:23525470)
• In conclusion, CEACAM19 showed high expression in tumor samples compared to normal mammary tissue. (PMID:27909883)
• High CEACAM19 expression is associated with gastric cancer. (PMID:30217308)
• Identification and expression analysis of novel splice variants of the human carcinoembryonic antigen-related cell adhesion molecule 19 (CEACAM19) gene using a high-throughput sequencing approach. (PMID:32659328)

Cross-species orthologs

10 orthologs

Organism	Symbol	Gene ID
danio_rerio	zgc:198329	ENSDARG00000076981
danio_rerio	si:dkey-250k15.8	ENSDARG00000078177
danio_rerio	si:ch211-264f5.6	ENSDARG00000079372
danio_rerio	si:dkey-250k15.10	ENSDARG00000092520
danio_rerio	si:dkey-11o1.3	ENSDARG00000093279
danio_rerio	si:dkey-250k15.7	ENSDARG00000095048
danio_rerio	si:dkey-250k15.9	ENSDARG00000095134
danio_rerio	si:dkey-11o1.2	ENSDARG00000095772
mus_musculus	Ceacam19	ENSMUSG00000049848
rattus_norvegicus	Ceacam19	ENSRNOG00000043088

Paralogs (24): CEACAM21 (ENSG00000007129), CEACAM7 (ENSG00000007306), CEACAM1 (ENSG00000079385), CEACAM6 (ENSG00000086548), CEACAM4 (ENSG00000105352), CEACAM5 (ENSG00000105388), PSG8 (ENSG00000124467), CEACAM8 (ENSG00000124469), HEPACAM (ENSG00000165478), PSG6 (ENSG00000170848), CEACAM3 (ENSG00000170956), PSG9 (ENSG00000183668), HEPACAM2 (ENSG00000188175), PSG5 (ENSG00000204941), CEACAM18 (ENSG00000213822), CEACAM16 (ENSG00000213892), VSTM5 (ENSG00000214376), PSG3 (ENSG00000221826), PSG7 (ENSG00000221878), PSG1 (ENSG00000231924), PSG2 (ENSG00000242221), PSG11 (ENSG00000243130), PSG4 (ENSG00000243137), CEACAM20 (ENSG00000273777)

Genomic neighbors (locus context)

Genes flanking this one on the chromosome (NCBI/Entrez gene neighborhood). Positional context only — some neighbors share regulatory elements (bidirectional promoters, antisense/overlapping transcripts), but chromosomal adjacency is not itself a functional relationship (see Interactions for that).

Symbol	Type	Entrez
IGSF23	protein-coding	147710
PVR	protein-coding	5817
MIR8085	ncRNA	102465879
CEACAM16	protein-coding	388551
BCL3	protein-coding	602
MIR4531	ncRNA	100616355
CEACAM16-AS1	ncRNA	107985305
CEACAM20	protein-coding	125931

Protein

Protein identifiers

Cell adhesion molecule CEACAM19 — Q7Z692 (reviewed: Q7Z692)

Alternative names: Carcinoembryonic antigen-like 1, Carcinoembryonic antigen-related cell adhesion molecule 19

All UniProt accessions (4): A0A087WWX9, A0A158VUY4, Q7Z692, K7EK61

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Tissue specificity. Ubiquitous with highest expression in prostate, uterus, fetal brain, mammary gland, adrenal gland, skeletal muscle, small intestine, and kidney, and lower expression in lung, cerebellum, testis, liver, pancreas, bone marrow and ovary.

Induction. Down-regulated by dexamethasone (in vitro).

Similarity. Belongs to the immunoglobulin superfamily. CEA family.

Isoforms (3)

UniProt ID	Names	Canonical?
Q7Z692-1	1	yes
Q7Z692-2	2
Q7Z692-3	3

RefSeq proteins (3): NP_001121365, NP_001376651, NP_064604 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR013106	Ig_V-set	Domain
IPR013783	Ig-like_fold	Homologous_superfamily
IPR036179	Ig-like_dom_sf	Homologous_superfamily
IPR050831	CEA_cell_adhesion	Family

Pfam: PF07686

UniProt features (10 total): splice variant 3, topological domain 2, signal peptide 1, chain 1, transmembrane region 1, region of interest 1, glycosylation site 1

Structure

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q7Z692-F1	69.95	0.37

Human Protein Atlas

Protein class: Predicted membrane proteins, Predicted intracellular proteins, UniProt - Evidence at transcript level

Protein evidence: Evidence at transcript level

Subcellular location (HPA, imaging): mitochondria; nucleoli; nucleoplasm

Antibody reliability (HPA): IH uncertain · IF approved

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Glycosylation sites (1)

Type	Positions
N-linked (glcnac…) asparagine	104

Function

Pathways and Gene Ontology

Reactome pathways

0 curated (TAS) of 0; 0 disease pathways. Curated-first; evidence = TAS (manually curated) vs IEA (electronic inference).

MSigDB gene sets: 44 (showing top): GSE37336_LY6C_POS_VS_NEG_NAIVE_CD4_TCELL_DN, GOBP_HETEROPHILIC_CELL_CELL_ADHESION, ROVERSI_GLIOMA_COPY_NUMBER_UP, GOBP_CELL_CELL_ADHESION, CDP_01, SRC_UP.V1_UP, CDP_02, GSE13522_CTRL_VS_T_CRUZI_BRAZIL_STRAIN_INF_SKIN_UP, CSHL1_TARGET_GENES, HES2_TARGET_GENES, TEAD2_TARGET_GENES, ZNF23_TARGET_GENES, ZNF362_TARGET_GENES, ZNF596_TARGET_GENES, ZNF92_TARGET_GENES

GO Biological Process (2): homophilic cell-cell adhesion (GO:0007156), heterophilic cell-cell adhesion (GO:0007157)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (2): plasma membrane (GO:0005886), membrane (GO:0016020)

GO top-level categories

5 GO namespaces:

Category	Terms
cell-cell adhesion	2
binding	1
membrane	1
cell periphery	1
cellular anatomical structure	1

Protein interactions and networks

STRING

showing 15 of 270 interactions by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CEACAM19	CEACAM18	A8MTB9	828
CEACAM19	CEACAM20	Q6UY09	746
CEACAM19	CEACAM21	Q3KPI0	603
CEACAM19	IGSF23	A1L1A6	501
CEACAM19	CLPTM1	O96005	498
CEACAM19	BCL3	P20749	488
CEACAM19	PPP1R37	O75864	484
CEACAM19	PRSS36	Q5K4E3	428
CEACAM19	LIPE	Q05469	427
CEACAM19	TRAPPC6A	O75865	399
CEACAM19	CEACAM7	Q14002	386
CEACAM19	PGLYRP1	O75594	381
CEACAM19	VTCN1	Q7Z7D3	370
CEACAM19	CD177	Q8N6Q3	370
CEACAM19	SIGLEC14	Q08ET2	364

IntAct

Human interaction partners of CEACAM19 in IntAct, one row per partner (best MIscore; records = supporting IntAct interaction records).

1 partners by confidence:

Partner	Interaction type	MIscore	Records
FSTL5	physical association	0.400	1

BioGRID (1 interactions; top human partners by supporting records): TRIM25 (Affinity Capture-RNA)

Disease & clinical

Genetic variants

Variant evidence for CEACAM19: 38 ClinVar records (1 pathogenic / likely pathogenic); 4 GWAS associations. Per-variant detail is on Sugi Variant.

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	27
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (1)

Showing all 1 pathogenic / likely-pathogenic ClinVar records, ranked by ClinVar review status (expert panel → multiple submitters → single submitter), then by number of submitting labs.

Variant ID	HGVS	Classification	Review	Submitters
816084	GRCh37/hg19 19q13.31-13.42(chr19:44738088-53621561)x3	Pathogenic	no assertion criteria provided	1

Per-variant reference — Sugi Variant

Explore CEACAM19’s pathogenic and likely-pathogenic variants individually — each with its ClinVar classification and conditions, applied ACMG criteria (ClinGen expert panel, where curated), the calibrated in-silico predictors (AlphaMissense, REVEL, SaProt, conservation), gnomAD frequency, and the predictor-disagreement QC signal — on Sugi Variant.

SpliceAI

Top 10 splice-impact sites by Δscore (adjacent positions with the same effect merged into one range; 34 predictions of 492):

Position(s)	Effect	Δscore	Sites
19:44672965–44672966	donor_loss	1.0000	5
19:44676263	acceptor_gain	1.0000
19:44676269	acceptor_loss	1.0000	2
19:44682565–44682566	acceptor_loss	1.0000	5
19:44682621–44682622	donor_loss	1.0000	4
19:44673860	donor_gain	0.9900
19:44676269–44676270	acceptor_loss	0.9900	3
19:44676422–44676423	donor_loss	0.9900	6
19:44680277	acceptor_gain	0.9900
19:44680286–44680287	acceptor_loss	0.9900	6

AlphaMissense

306 missense substitutions predicted likely pathogenic (of 1,928 scored), across 96 residues. Top 20 hotspot residues, ranked by the number of likely-pathogenic substitutions (of those reachable by a single-nucleotide change), then by mean score:

Residue	Likely-pathogenic substitutions	Mean am_pathogenicity	Max am_pathogenicity
F78	8	0.900	0.976
D116	8	0.900	0.943
W65	7	0.972	0.993
F102	7	0.947	0.972
D90	7	0.665	0.772
P40	6	0.894	0.938
M107	6	0.883	0.933
G68	6	0.844	0.935
G105	6	0.838	0.984
Q88	6	0.782	0.956
Y120	5	0.952	0.989
Y66	5	0.882	0.934
S106	5	0.863	0.988
G91	5	0.858	0.918
G101	5	0.841	0.969
R89	5	0.826	0.924
P43	5	0.825	0.955
W130	5	0.813	0.901
L51	5	0.811	0.970
I36	5	0.808	0.944

HPA cancer prognostics

RNA cancer specificity: Low cancer specificity

Human Protein Atlas survival analysis — favorable = higher expression predicts better survival.

1 prognostic cancer types:

Cancer	Prognostic	p-value
Kidney Renal Papillary Cell Carcinoma (TCGA)	unfavorable	0.000145

Disease associations

OMIM: gene MIM:606691 | disease phenotypes:

GWAS associations

4 associations:

Study	Trait	p-value
GCST007827_5	Alzheimer’s disease or HDL levels (pleiotropy)	7e-74
GCST007827_6	Alzheimer’s disease or HDL levels (pleiotropy)	7e-54
GCST007827_8	Alzheimer’s disease or HDL levels (pleiotropy)	3e-36
GCST007827_17	Alzheimer’s disease or HDL levels (pleiotropy)	3e-12

EFO canonical traits (from GWAS)

1 canonical traits:

EFO ID	Trait name
EFO:0004612	high density lipoprotein cholesterol measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (CPIC guideline: no)

CTD chemical–gene interactions

22 total (human), top 22 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	decreases expression, decreases methylation	3
aristolochic acid I	increases expression	1
fluorene-9-bisphenol	increases expression	1
triphenyl phosphate	affects expression	1
2,5,2’,5’-tetrachlorobiphenyl	increases expression	1
sodium arsenite	decreases expression	1
abrine	increases expression	1
jinfukang	affects cotreatment, decreases expression	1
2,3,5-trichloro-6-phenyl-(1,4)benzoquinone	decreases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Sunitinib	increases expression	1
Air Pollutants	increases abundance, increases expression	1
Arsenic	affects methylation	1
Cisplatin	decreases expression, affects cotreatment	1
Dimethyl Sulfoxide	affects expression	1
Plant Extracts	decreases expression, affects cotreatment	1
Smoke	decreases expression	1
Aflatoxin B1	increases methylation	1
Cadmium Chloride	increases expression	1
Copper Sulfate	increases expression	1
Lactic Acid	decreases expression	1
Particulate Matter	increases abundance, increases expression	1

Clinical trials (associated diseases)

Via MONDO — disease-level, not drug-specific.