SHISAL2B

Summary

SHISAL2B (shisa like 2B, HGNC:34236) is a protein-coding gene on chromosome 5q12.3, encoding Protein shisa-like-2B (A6NKW6).

Predicted to be located in membrane.

Source: NCBI Gene 100132916 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 38 total
• MANE Select transcript: NM_001164442

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:34236
Approved symbol	SHISAL2B
Name	shisa like 2B
Location	5q12.3
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000145642
Ensembl biotype	protein_coding
OMIM	620219
Entrez	100132916

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 2 nonsense_mediated_decay, 2 protein_coding_CDS_not_defined, 1 protein_coding

ENST00000389074, ENST00000506473, ENST00000509189, ENST00000512767, ENST00000513930

RefSeq mRNA: 1 — MANE Select: NM_001164442 NM_001164442

CCDS: CCDS47220

Canonical transcript exons

ENST00000389074 — 3 exons

Exon	Start	End
ENSE00002066700	64690503	64690814
ENSE00002085942	64717889	64718190
ENSE00003605526	64695507	64695664

Expression profiles

Bgee: expression breadth broad, 90 present calls, max score 87.76.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.6103 / max 62.5621, expressed in 145 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
56676	0.3880	125
56675	0.2224	73

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
islet of Langerhans	UBERON:0000006	87.76	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	81.92	gold quality
pancreas	UBERON:0001264	78.45	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	75.45	gold quality
body of pancreas	UBERON:0001150	74.28	gold quality
hypothalamus	UBERON:0001898	63.04	gold quality
nucleus accumbens	UBERON:0001882	53.64	gold quality
putamen	UBERON:0001874	52.27	gold quality
placenta	UBERON:0001987	51.86	gold quality
ventricular zone	UBERON:0003053	50.60	gold quality
duodenum	UBERON:0002114	49.73	gold quality
caudate nucleus	UBERON:0001873	48.09	gold quality
Ammon’s horn	UBERON:0001954	45.58	gold quality
amygdala	UBERON:0001876	42.89	gold quality
temporal lobe	UBERON:0001871	42.70	gold quality
granulocyte	CL:0000094	42.58	silver quality
right ovary	UBERON:0002118	42.52	gold quality
hindlimb stylopod muscle	UBERON:0004252	42.43	gold quality
ovary	UBERON:0000992	42.25	gold quality
left ovary	UBERON:0002119	41.79	gold quality
substantia nigra	UBERON:0002038	41.75	gold quality
right testis	UBERON:0004534	40.20	gold quality
brain	UBERON:0000955	39.81	gold quality
right coronary artery	UBERON:0001625	39.80	silver quality
testis	UBERON:0000473	39.79	gold quality
endometrium	UBERON:0001295	39.03	silver quality
left testis	UBERON:0004533	38.70	gold quality
ganglionic eminence	UBERON:0004023	38.13	gold quality
calcaneal tendon	UBERON:0003701	38.11	silver quality
colonic epithelium	UBERON:0000397	37.20	gold quality

Single-cell (SCXA)

Detected in 8 experiment(s), a significant marker in 8.

Experiment	Marker?	Max mean expression
E-HCAD-31	yes	1777.66
E-GEOD-81547	yes	587.40
E-GEOD-83139	yes	186.38
E-MTAB-5061	yes	19.32
E-GEOD-81608	yes	17.02
E-ENAD-27	yes	11.59
E-MTAB-9388	yes	8.32
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

35 targeting SHISAL2B, 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-3925-3P	100.00	69.95	1237
HSA-MIR-559	99.95	72.28	3609
HSA-MIR-548AB	99.95	71.31	3488
HSA-MIR-548A-5P	99.94	71.27	3482
HSA-MIR-548AD-5P	99.94	71.23	3502
HSA-MIR-548AE-5P	99.94	71.23	3502
HSA-MIR-548AK	99.94	71.24	3488
HSA-MIR-548AM-5P	99.94	71.24	3488
HSA-MIR-548AP-5P	99.94	71.14	3489
HSA-MIR-548AQ-5P	99.94	71.34	3426
HSA-MIR-548AR-5P	99.94	71.28	3515
HSA-MIR-548AS-5P	99.94	71.22	3482
HSA-MIR-548AU-5P	99.94	71.24	3488
HSA-MIR-548AY-5P	99.94	71.23	3502
HSA-MIR-548B-5P	99.94	71.23	3502
HSA-MIR-548BB-5P	99.94	71.27	3509
HSA-MIR-548C-5P	99.94	71.24	3488
HSA-MIR-548D-5P	99.94	71.23	3502
HSA-MIR-548H-5P	99.94	71.24	3488
HSA-MIR-548I	99.94	71.25	3481
HSA-MIR-548J-5P	99.94	71.14	3489
HSA-MIR-548O-5P	99.94	71.24	3488
HSA-MIR-548W	99.94	71.24	3488
HSA-MIR-548Y	99.94	71.28	3514
HSA-MIR-6845-3P	99.94	66.88	1439
HSA-MIR-548E-5P	99.89	72.73	4486
HSA-MIR-142-5P	99.48	70.92	2416
HSA-MIR-5590-3P	99.48	70.91	2429
HSA-MIR-4711-3P	98.97	66.87	1020
HSA-MIR-4703-5P	98.53	70.13	1645

Literature-anchored findings (GeneRIF, showing 2)

• Immunohistochemical Evaluation of Adaptor Protein FAM159B Expression in Normal and Neoplastic Human Tissues. (PMID:34830137)
• Co-Expression of Adaptor Protein FAM159B with Different Markers for Neuroendocrine Cells: An Immunocytochemical and Immunohistochemical Study. (PMID:36362289)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Shisal2b	ENSMUSG00000042655
rattus_norvegicus	Shisal2b	ENSRNOG00000013372

Paralogs (5): SHISAL1 (ENSG00000138944), SHISA3 (ENSG00000178343), SHISA2 (ENSG00000180730), SHISAL2A (ENSG00000182183), SHISA4 (ENSG00000198892)

Protein

Protein identifiers

Protein shisa-like-2B — A6NKW6 (reviewed: A6NKW6)

All UniProt accessions (2): A6NKW6, D6RH14

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Similarity. Belongs to the shisa family.

RefSeq proteins (1): NP_001157914* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR026910	Shisa	Family
IPR053891	Shisa_N	Domain

Pfam: PF13908

UniProt features (4 total): sequence variant 2, chain 1, transmembrane region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A6NKW6-F1	69.22	0.24

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 35 (showing top): GSE45365_NK_CELL_VS_BCELL_DN, chr5q12, MEISSNER_NPC_HCP_WITH_H3_UNMETHYLATED, YAUCH_HEDGEHOG_SIGNALING_PARACRINE_UP, MEISSNER_BRAIN_HCP_WITH_H3K4ME3_AND_H3K27ME3, BRUINS_UVC_RESPONSE_VIA_TP53_GROUP_B, BRUINS_UVC_RESPONSE_MIDDLE, HAND1_TARGET_GENES, HES2_TARGET_GENES, ZNF528_TARGET_GENES, MIR431_5P, MIR210_3P, GSE14350_TREG_VS_TEFF_IN_IL2RB_KO_DN, MURARO_PANCREAS_BETA_CELL, MURARO_PANCREAS_PANCREATIC_POLYPEPTIDE_CELL

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

252 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SHISAL2B	C3orf22	Q8N5N4	540
SHISAL2B	RGS9	O75916	506
SHISAL2B	RNASE12	Q5GAN4	506
SHISAL2B	SMIM17	P0DL12	479
SHISAL2B	C12orf56	Q8IXR9	479
SHISAL2B	SH2D7	A6NKC9	447
SHISAL2B	C22orf42	Q6IC83	446
SHISAL2B	C1orf167	Q5SNV9	446
SHISAL2B	CC2D2B	Q6DHV5	446
SHISAL2B	ANKRD62	A6NC57	445
SHISAL2B	TMEM182	Q6ZP80	441
SHISAL2B	NAA20	P61599	440
SHISAL2B	CLPSL1	A2RUU4	434
SHISAL2B	SPDYE4	A6NLX3	432
SHISAL2B	EPCIP	Q9NYP8	432

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A0A888, A0ZSE6, A0ZT23, A5PLF5, A5PLH4, A6NKW6, A6QQ93, A8WP66, D3YUK8, F1QYC4, F5HFG3, G5ED05, O17386, O39920, O45879, O62301, O74737, P02816, P0C5E7, P34298, P34389, P57054, P60987, P60988, P60990, Q01001, Q07FZ2, Q10128, Q10287, Q10351, Q18593, Q25197, Q6DE06, Q7SY31, Q8BJ83, Q8IMZ9, Q8VYA1, Q95PJ8, Q95QZ5, Q9BRN9

Diamond homologs: A2A9G7, A6NKW6, A6QQ93, Q6UWV7, Q9D1Y9, Q2WFL8

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	37
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

652 predictions. Top by Δscore:

Variant	Effect	Δscore
5:64695506:GC:G	acceptor_gain	1.0000
5:64695506:GCATT:G	acceptor_gain	1.0000
5:64717888:GGCAA:G	acceptor_gain	1.0000
5:64690797:C:G	donor_gain	0.9900
5:64695505:A:AG	acceptor_gain	0.9900
5:64695506:G:GA	acceptor_gain	0.9900
5:64695660:AGAAG:A	donor_loss	0.9900
5:64695661:GAAG:G	donor_gain	0.9900
5:64695661:GAAGG:G	donor_loss	0.9900
5:64695662:AAGGT:A	donor_loss	0.9900
5:64695663:AGGTA:A	donor_loss	0.9900
5:64695664:GG:G	donor_loss	0.9900
5:64695665:G:A	donor_loss	0.9900
5:64695666:T:C	donor_loss	0.9900
5:64717883:CTGCA:C	acceptor_loss	0.9900
5:64717884:TGCAG:T	acceptor_loss	0.9900
5:64717885:GCAGG:G	acceptor_loss	0.9900
5:64717886:CAG:C	acceptor_loss	0.9900
5:64717887:A:AG	acceptor_gain	0.9900
5:64717888:G:A	acceptor_loss	0.9900
5:64717888:G:GG	acceptor_gain	0.9900
5:64717888:GGCA:G	acceptor_gain	0.9900
5:64690896:G:T	donor_gain	0.9800
5:64695505:A:AT	acceptor_loss	0.9800
5:64695506:G:GT	acceptor_loss	0.9800
5:64695506:GCAT:G	acceptor_gain	0.9800
5:64717888:GGC:G	acceptor_gain	0.9800
5:64691407:G:GC	acceptor_gain	0.9700
5:64695508:ATT:A	acceptor_gain	0.9700
5:64717878:T:TA	acceptor_gain	0.9700

AlphaMissense

1043 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
5:64690738:T:C	F39L	0.998
5:64690739:T:G	F39C	0.998
5:64690740:C:A	F39L	0.998
5:64690740:C:G	F39L	0.998
5:64690735:G:T	G38C	0.997
5:64690781:T:G	F53C	0.997
5:64695565:A:C	S84R	0.997
5:64695567:T:A	S84R	0.997
5:64695567:T:G	S84R	0.997
5:64690693:T:A	C24S	0.996
5:64690694:G:C	C24S	0.996
5:64690731:C:G	C36W	0.996
5:64690688:T:G	F22C	0.995
5:64690693:T:C	C24R	0.995
5:64690730:G:A	C36Y	0.995
5:64690733:G:A	C37Y	0.995
5:64690758:C:G	C45W	0.995
5:64690760:G:A	C46Y	0.995
5:64690761:C:G	C46W	0.995
5:64690729:T:A	C36S	0.994
5:64690730:G:C	C36S	0.994
5:64690732:T:A	C37S	0.994
5:64690733:G:C	C37S	0.994
5:64690734:C:G	C37W	0.994
5:64690729:T:C	C36R	0.993
5:64690756:T:A	C45S	0.993
5:64690756:T:C	C45R	0.993
5:64690757:G:A	C45Y	0.993
5:64690757:G:C	C45S	0.993
5:64690759:T:A	C46S	0.993

dbSNP variants (sampled 300 via entrez): RS1000289536 (5:64695850 G>A), RS1000620794 (5:64694383 T>C), RS1000728644 (5:64715588 A>G), RS1000739943 (5:64715435 AAGG>A), RS1000794357 (5:64715214 C>G), RS1000804080 (5:64707399 G>A,T), RS1001138112 (5:64700678 G>A,C,T), RS1001287130 (5:64714879 A>G,T), RS1001487547 (5:64700343 A>T), RS1001586664 (5:64701525 G>A), RS1001666206 (5:64689136 AG>A), RS1001848954 (5:64693298 C>T), RS1001913476 (5:64700008 C>A,G), RS1001967318 (5:64700309 T>C), RS1001974655 (5:64701564 G>A)

Disease associations

OMIM: gene MIM:620219 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST004904_22	Body mass index	6.000000e-09

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004340	body mass index

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

9 total (human), top 9 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
propionaldehyde	increases expression	1
butyraldehyde	increases expression	1
benzo(e)pyrene	increases methylation	1
pentanal	increases expression	1
Aldehydes	increases expression	1
Benzo(a)pyrene	increases methylation	1
Methapyrilene	increases methylation	1
Thiram	increases expression	1
Cadmium Chloride	decreases expression	1

Clinical trials (associated diseases)

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