SHISAL1

Summary

SHISAL1 (shisa like 1, HGNC:29335) is a protein-coding gene on chromosome 22q13.31, encoding Protein shisa-like-1 (Q3SXP7).

Predicted to be located in membrane.

Source: NCBI Gene 85352 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 32 total
• MANE Select transcript: NM_001099294

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:29335
Approved symbol	SHISAL1
Name	shisa like 1
Location	22q13.31
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000138944
Ensembl biotype	protein_coding
OMIM	620220
Entrez	85352

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000381176

RefSeq mRNA: 1 — MANE Select: NM_001099294 NM_001099294

CCDS: CCDS43025

Canonical transcript exons

ENST00000381176 — 5 exons

Exon	Start	End
ENSE00001541363	44243665	44249685
ENSE00001541372	44300879	44300977
ENSE00001541373	44312751	44312951
ENSE00002238739	44285428	44285745
ENSE00002249981	44296672	44296885

Expression profiles

Bgee: expression breadth ubiquitous, 200 present calls, max score 96.97.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.1514 / max 34.6375, expressed in 44 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
194529	0.0637	27
194528	0.0304	9
194527	0.0276	14
194526	0.0183	8
194525	0.0114	6

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
lateral nuclear group of thalamus	UBERON:0002736	96.97	gold quality
orbitofrontal cortex	UBERON:0004167	92.77	gold quality
middle temporal gyrus	UBERON:0002771	92.22	gold quality
Brodmann (1909) area 46	UBERON:0006483	92.20	gold quality
entorhinal cortex	UBERON:0002728	91.73	gold quality
CA1 field of hippocampus	UBERON:0003881	91.21	gold quality
superior frontal gyrus	UBERON:0002661	90.90	gold quality
cortical plate	UBERON:0005343	90.85	gold quality
Brodmann (1909) area 23	UBERON:0013554	90.80	gold quality
myometrium	UBERON:0001296	89.66	gold quality
temporal lobe	UBERON:0001871	88.67	gold quality
endothelial cell	CL:0000115	88.39	gold quality
frontal cortex	UBERON:0001870	88.37	gold quality
body of uterus	UBERON:0009853	88.25	gold quality
prefrontal cortex	UBERON:0000451	88.13	gold quality
anterior cingulate cortex	UBERON:0009835	88.01	gold quality
cingulate cortex	UBERON:0003027	87.97	gold quality
neocortex	UBERON:0001950	87.67	gold quality
smooth muscle tissue	UBERON:0001135	87.65	gold quality
postcentral gyrus	UBERON:0002581	87.54	gold quality
right frontal lobe	UBERON:0002810	87.06	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	87.04	gold quality
amygdala	UBERON:0001876	86.94	gold quality
parietal lobe	UBERON:0001872	86.78	gold quality
cerebral cortex	UBERON:0000956	86.40	gold quality
dorsal plus ventral thalamus	UBERON:0001897	84.80	gold quality
hypothalamus	UBERON:0001898	84.65	gold quality
Brodmann (1909) area 9	UBERON:0013540	84.51	gold quality
muscle layer of sigmoid colon	UBERON:0035805	83.42	gold quality
endocervix	UBERON:0000458	82.92	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-GEOD-81608	yes	92.33
E-GEOD-124858	no	86.76
E-ANND-3	no	2.35

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

327 targeting SHISAL1, 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-4795-3P	100.00	74.62	4024
HSA-MIR-126-5P	100.00	72.71	3180
HSA-MIR-8485	100.00	77.57	4731
HSA-MIR-6867-5P	100.00	82.21	3464
HSA-MIR-7110-3P	100.00	73.18	2486
HSA-MIR-29A-3P	100.00	73.11	1835
HSA-MIR-29B-3P	100.00	73.18	1833
HSA-MIR-29C-3P	100.00	73.15	1833
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-4510	100.00	66.60	2050
HSA-MIR-6127	100.00	66.76	2188
HSA-MIR-6129	100.00	66.46	2080
HSA-MIR-6130	100.00	66.69	2012
HSA-MIR-6133	100.00	66.48	2064
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-4682	100.00	68.89	1258
HSA-MIR-5193	100.00	67.26	1744
HSA-MIR-513A-5P	100.00	69.77	2465
HSA-MIR-4283	100.00	66.42	2097
HSA-MIR-4673	100.00	66.64	1490
HSA-MIR-3162-3P	100.00	65.37	363
HSA-MIR-6870-5P	99.99	68.55	2115
HSA-MIR-3667-3P	99.99	67.17	1636
HSA-MIR-34A-5P	99.99	71.21	1784
HSA-MIR-449A	99.99	71.05	1776
HSA-MIR-513B-5P	99.99	69.96	2150
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-4645-5P	99.98	65.81	1284
HSA-MIR-27A-3P	99.98	72.13	2955
HSA-MIR-27B-3P	99.98	72.13	2955

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	shisal1a	ENSDARG00000045594
danio_rerio	shisal1b	ENSDARG00000067710
mus_musculus	Shisal1	ENSMUSG00000062760
rattus_norvegicus		ENSRNOG00000078763

Paralogs (5): SHISAL2B (ENSG00000145642), SHISA3 (ENSG00000178343), SHISA2 (ENSG00000180730), SHISAL2A (ENSG00000182183), SHISA4 (ENSG00000198892)

Protein

Protein identifiers

Protein shisa-like-1 — Q3SXP7 (reviewed: Q3SXP7)

All UniProt accessions (1): Q3SXP7

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Similarity. Belongs to the shisa family.

RefSeq proteins (1): NP_001092764* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR026910	Shisa	Family
IPR053891	Shisa_N	Domain

Pfam: PF13908

UniProt features (11 total): topological domain 2, compositionally biased region 2, glycosylation site 2, signal peptide 1, chain 1, sequence conflict 1, transmembrane region 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q3SXP7-F1	67.98	0.04

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 (2): 53, 95

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 91 (showing top): GSE45365_NK_CELL_VS_CD11B_DC_UP, PEREZ_TP63_TARGETS, ROZANOV_MMP14_TARGETS_UP, PEREZ_TP53_AND_TP63_TARGETS, chr22q13, KYNG_WERNER_SYNDROM_AND_NORMAL_AGING_UP, BRUINS_UVC_RESPONSE_VIA_TP53_GROUP_A, GOBERT_OLIGODENDROCYTE_DIFFERENTIATION_DN, ZWANG_TRANSIENTLY_UP_BY_2ND_EGF_PULSE_ONLY, PRC2_EZH2_UP.V1_UP, NAKAYAMA_SOFT_TISSUE_TUMORS_PCA2_UP, MIR8485, MIR6867_5P, MIR548AJ_3P_MIR548X_3P, MIR548AE_3P_MIR548AQ_3P

GO Biological Process (0):

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

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

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1
cellular anatomical structure	1

Protein interactions and networks

STRING

402 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SHISAL1	SHISAL2A	Q6UWV7	579
SHISAL1	FAM184A	Q8NB25	543
SHISAL1	CYYR1	Q96J86	503
SHISAL1	LLPH	Q9BRT6	484
SHISAL1	WBP1	Q96G27	452
SHISAL1	SHISA3	A0PJX4	427
SHISAL1	VOPP1	Q96AW1	408
SHISAL1	CCDC9B	Q6ZUT6	397
SHISAL1	SMPDL3A	Q92484	377
SHISAL1	SHISAL2B	A6NKW6	375
SHISAL1	ZNF226	Q9NYT6	371
SHISAL1	FAM217B	Q9NTX9	370
SHISAL1	LYPD1	Q8N2G4	360
SHISAL1	DENND2A	Q9ULE3	355
SHISAL1	TSPYL4	Q9UJ04	354

IntAct

86 interactions, top by confidence:

A	B	Type	Score
SLC41A2	SHISAL1	psi-mi:“MI:0915”(physical association)	0.560
ALG10	SHISAL1	psi-mi:“MI:0915”(physical association)	0.560
SLC35B2	SHISAL1	psi-mi:“MI:0915”(physical association)	0.560
ZFPL1	SHISAL1	psi-mi:“MI:0915”(physical association)	0.560
PLPP6	SHISAL1	psi-mi:“MI:0915”(physical association)	0.560
ARLN	SHISAL1	psi-mi:“MI:0915”(physical association)	0.560
LPAR3	SHISAL1	psi-mi:“MI:0915”(physical association)	0.560
GPR25	SHISAL1	psi-mi:“MI:0915”(physical association)	0.560
SLC38A7	SHISAL1	psi-mi:“MI:0915”(physical association)	0.560
SLC16A13	SHISAL1	psi-mi:“MI:0915”(physical association)	0.560
ALG10B	SHISAL1	psi-mi:“MI:0915”(physical association)	0.560
SLC52A1	SHISAL1	psi-mi:“MI:0915”(physical association)	0.560
SLC39A7	SHISAL1	psi-mi:“MI:0915”(physical association)	0.560
GJB2	SHISAL1	psi-mi:“MI:0915”(physical association)	0.560
SHISAL1	MFSD6	psi-mi:“MI:0915”(physical association)	0.560
SHISAL1	MFF	psi-mi:“MI:0915”(physical association)	0.560
SHISAL1	SLC16A13	psi-mi:“MI:0915”(physical association)	0.560
SHISAL1	SLC41A2	psi-mi:“MI:0915”(physical association)	0.560
SHISAL1	ALG10	psi-mi:“MI:0915”(physical association)	0.560
SHISAL1	SCAMP5	psi-mi:“MI:0915”(physical association)	0.560
ASPH	SHISAL1	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (59): KIAA1644 (Affinity Capture-RNA), KIAA1644 (Affinity Capture-RNA), KIAA1644 (Two-hybrid), KIAA1644 (Two-hybrid), KIAA1644 (Two-hybrid), KIAA1644 (Two-hybrid), KIAA1644 (Two-hybrid), KIAA1644 (Two-hybrid), KIAA1644 (Two-hybrid), ALG10 (Two-hybrid), TMEM140 (Two-hybrid), MFSD6 (Two-hybrid), SLC35B2 (Two-hybrid), CYB561A3 (Two-hybrid), ZFPL1 (Two-hybrid)

ESM2 similar proteins: A0A1B0GVV1, A0M8S0, A0M8T1, A0M8U1, A3KN28, A4D7R9, A9JRA0, B1AZA5, E9Q2Z6, P01134, P48030, Q00PJ0, Q07DV5, Q07DW9, Q07DX8, Q07DY8, Q07E08, Q07E45, Q09YH4, Q09YI5, Q09YJ7, Q09YK8, Q09YN2, Q108U3, Q1RLU8, Q2IBA8, Q2IBD0, Q2IBE0, Q2IBE8, Q2PG42, Q2QL86, Q2QLA6, Q2QLB7, Q2QLD7, Q2QLE8, Q2QLG2, Q3KRC4, Q3SXP7, Q5T292, Q68FW3

Diamond homologs: Q0VBP7, Q1RMB5, Q3SXP7

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	30
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1106 predictions. Top by Δscore:

Variant	Effect	Δscore
22:44249563:T:TA	donor_gain	1.0000
22:44296670:A:AC	donor_gain	1.0000
22:44296671:C:CC	donor_gain	1.0000
22:44303903:C:CA	donor_gain	1.0000
22:44285741:AATTG:A	acceptor_gain	0.9900
22:44285742:ATTG:A	acceptor_gain	0.9900
22:44285742:ATTGC:A	acceptor_loss	0.9900
22:44285743:TTG:T	acceptor_gain	0.9900
22:44285743:TTGCT:T	acceptor_loss	0.9900
22:44285744:TG:T	acceptor_gain	0.9900
22:44285745:GCTG:G	acceptor_loss	0.9900
22:44285746:C:CC	acceptor_gain	0.9900
22:44285746:C:CG	acceptor_loss	0.9900
22:44285747:T:G	acceptor_loss	0.9900
22:44296664:GCACT:G	donor_loss	0.9900
22:44296665:CACT:C	donor_loss	0.9900
22:44296666:ACTCA:A	donor_loss	0.9900
22:44296667:CT:C	donor_loss	0.9900
22:44296668:TCAC:T	donor_loss	0.9900
22:44296669:CACTT:C	donor_loss	0.9900
22:44296670:A:T	donor_loss	0.9900
22:44296671:CTT:C	donor_gain	0.9900
22:44296881:CAAGA:C	acceptor_gain	0.9900
22:44296882:AAGA:A	acceptor_gain	0.9900
22:44296886:C:CC	acceptor_gain	0.9900
22:44312748:TA:T	donor_loss	0.9900
22:44312749:ACC:A	donor_loss	0.9900
22:44249517:T:C	donor_gain	0.9800
22:44249560:T:TA	donor_gain	0.9800
22:44296663:GGCAC:G	donor_loss	0.9800

AlphaMissense

1296 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
22:44296818:G:C	F45L	0.998
22:44296818:G:T	F45L	0.998
22:44296820:A:G	F45L	0.998
22:44296812:G:C	C47W	0.996
22:44296814:A:G	C47R	0.996
22:44296819:A:C	F45C	0.996
22:44296819:A:G	F45S	0.996
22:44296741:C:T	C71Y	0.995
22:44296743:G:C	C70W	0.995
22:44296773:A:C	C60W	0.995
22:44296813:C:G	C47S	0.995
22:44296814:A:T	C47S	0.995
22:44296861:C:T	C31Y	0.995
22:44296740:G:C	C71W	0.994
22:44296744:C:T	C70Y	0.994
22:44296774:C:G	C60S	0.994
22:44296774:C:T	C60Y	0.994
22:44296775:A:G	C60R	0.994
22:44296775:A:T	C60S	0.994
22:44296813:C:T	C47Y	0.994
22:44296862:A:G	C31R	0.994
22:44285711:C:G	G106R	0.993
22:44285711:C:T	G106R	0.993
22:44296777:C:G	C59S	0.993
22:44296778:A:G	C59R	0.993
22:44296778:A:T	C59S	0.993
22:44296861:C:G	C31S	0.993
22:44296862:A:T	C31S	0.993
22:44296741:C:G	C71S	0.992
22:44296742:A:G	C71R	0.992

dbSNP variants (sampled 300 via entrez): RS1000022620 (22:44283144 G>A), RS1000023444 (22:44314127 C>G), RS1000045153 (22:44299288 C>T), RS1000143667 (22:44281750 T>A), RS1000197417 (22:44280678 A>C,T), RS1000208929 (22:44264441 G>A,C), RS1000253450 (22:44273111 A>G), RS1000290667 (22:44328190 T>A), RS1000311272 (22:44308344 C>T), RS1000404347 (22:44308558 G>T), RS1000420209 (22:44247461 T>G), RS1000420921 (22:44303216 A>T), RS1000445292 (22:44333116 G>A,C), RS1000466595 (22:44333028 A>G), RS1000473185 (22:44268895 G>A)

Disease associations

OMIM: gene MIM:620220 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

3 associations (top):

Study	Trait	p-value
GCST003542_170	Night sleep phenotypes	7.000000e-06
GCST008179_19	Moderate-to-late spontaneous preterm birth	9.000000e-08
GCST009856_36	Leukocyte telomere length	3.000000e-06

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0006917	spontaneous preterm birth

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

40 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	decreases expression, affects expression, increases methylation, affects cotreatment	7
sodium arsenite	decreases expression, affects cotreatment, increases abundance, increases expression	3
Benzo(a)pyrene	decreases expression, decreases methylation, affects methylation	3
mercuric bromide	decreases expression, affects cotreatment	2
entinostat	decreases expression, affects cotreatment	2
belinostat	decreases expression, affects cotreatment	2
Vorinostat	affects cotreatment, decreases expression	2
Arsenic	affects cotreatment, increases abundance, decreases expression	2
Nickel	increases expression	2
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
Aflatoxin B1	decreases methylation, increases methylation	2
p-Chloromercuribenzoic Acid	affects cotreatment, decreases expression	2
Particulate Matter	increases abundance, increases expression	2
trichostatin A	decreases expression	1
arsenite	affects binding, decreases reaction	1
manganese chloride	affects cotreatment, decreases expression, increases abundance	1
benzo(e)pyrene	affects methylation	1
aflatoxin B2	affects methylation	1
nickel sulfate	increases expression	1
S-(1,2-dichlorovinyl)cysteine	increases expression, affects response to substance	1
pentanal	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
(+)-JQ1 compound	decreases expression	1
Temozolomide	decreases expression	1
Sunitinib	increases expression	1
Air Pollutants	increases expression, increases abundance	1
Carbamazepine	affects expression	1
Dichlorodiphenyl Dichloroethylene	increases expression	1
Doxorubicin	decreases expression	1

Clinical trials (associated diseases)

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