SHROOM1

Summary

SHROOM1 (shroom family member 1, HGNC:24084) is a protein-coding gene on chromosome 5q31.1, encoding Protein Shroom1 (Q2M3G4). May be involved in the assembly of microtubule arrays during cell elongation.

SHROOM family members play diverse roles in the development of the nervous system and other tissues (Hagens et al., 2006 [PubMed 16615870]).

Source: NCBI Gene 134549 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 122 total
• MANE Select transcript: NM_001172700

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:24084
Approved symbol	SHROOM1
Name	shroom family member 1
Location	5q31.1
Locus type	gene with protein product
Status	Approved
Aliases	APXL2, KIAA1960
Ensembl gene	ENSG00000164403
Ensembl biotype	protein_coding
OMIM	611179
Entrez	134549

Gene structure

Transcript identifiers

Ensembl transcripts: 40 — 37 protein_coding, 2 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000319854, ENST00000378676, ENST00000378679, ENST00000440118, ENST00000488072, ENST00000495680, ENST00000606676, ENST00000617339, ENST00000891704, ENST00000891705, ENST00000891706, ENST00000891707, ENST00000891708, ENST00000891709, ENST00000891710, ENST00000891711, ENST00000891712, ENST00000891713, ENST00000891714, ENST00000891715, ENST00000891716, ENST00000891717, ENST00000924501, ENST00000924502, ENST00000949960, ENST00000949961, ENST00000949962, ENST00000949963, ENST00000949964, ENST00000949965, ENST00000949966, ENST00000949967, ENST00000949968, ENST00000949969, ENST00000949970, ENST00000949971, ENST00000949972, ENST00000949973, ENST00000949974, ENST00000949975

RefSeq mRNA: 3 — MANE Select: NM_001172700 NM_001172700, NM_001410779, NM_133456

CCDS: CCDS4161, CCDS54902, CCDS93780

Canonical transcript exons

ENST00000378679 — 10 exons

Exon	Start	End
ENSE00001084096	132823850	132824419
ENSE00001084099	132823250	132823522
ENSE00001084101	132823623	132823764
ENSE00001169579	132824615	132824821
ENSE00001169587	132825018	132825073
ENSE00001415418	132825163	132826182
ENSE00001478390	132826277	132826587
ENSE00001478392	132827461	132827607
ENSE00001478394	132830594	132830647
ENSE00001924838	132822141	132823128

Expression profiles

Bgee: expression breadth ubiquitous, 242 present calls, max score 96.30.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 4.4484 / max 109.8884, expressed in 1435 samples.

FANTOM5 promoters (7 alternative TSS)

Promoter ID	TPM avg	Samples expressed
63366	3.5243	1318
63372	0.4368	196
63371	0.1473	61
63368	0.1462	52
63367	0.1075	34
63370	0.0536	12
63369	0.0327	13

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
pancreatic ductal cell	CL:0002079	96.30	gold quality
right lobe of liver	UBERON:0001114	96.11	gold quality
kidney epithelium	UBERON:0004819	95.88	silver quality
mucosa of transverse colon	UBERON:0004991	95.88	gold quality
seminal vesicle	UBERON:0000998	94.98	gold quality
left ventricle myocardium	UBERON:0006566	94.65	silver quality
medial globus pallidus	UBERON:0002477	93.80	gold quality
prostate gland	UBERON:0002367	93.73	gold quality
epithelial cell of pancreas	CL:0000083	93.71	silver quality
liver	UBERON:0002107	93.21	gold quality
inferior vagus X ganglion	UBERON:0005363	93.19	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	92.99	gold quality
globus pallidus	UBERON:0001875	92.90	gold quality
subthalamic nucleus	UBERON:0001906	92.77	gold quality
spinal cord	UBERON:0002240	92.63	gold quality
nasal cavity epithelium	UBERON:0005384	92.52	silver quality
ventral tegmental area	UBERON:0002691	91.61	gold quality
ileal mucosa	UBERON:0000331	91.03	gold quality
dorsal plus ventral thalamus	UBERON:0001897	90.97	gold quality
medulla oblongata	UBERON:0001896	90.95	gold quality
substantia nigra pars reticulata	UBERON:0001966	90.68	gold quality
colonic mucosa	UBERON:0000317	90.48	gold quality
pons	UBERON:0000988	90.35	gold quality
endothelial cell	CL:0000115	90.33	gold quality
midbrain	UBERON:0001891	90.28	gold quality
substantia nigra	UBERON:0002038	90.17	gold quality
cardia of stomach	UBERON:0001162	89.75	gold quality
superior vestibular nucleus	UBERON:0007227	89.55	gold quality
transverse colon	UBERON:0001157	89.54	gold quality
urinary bladder	UBERON:0001255	89.51	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	13.79
E-MTAB-6142	no	19.77

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

14 targeting SHROOM1, 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-6748-5P	100.00	65.81	1057
HSA-MIR-302E	99.96	70.74	2669
HSA-MIR-5584-5P	99.49	68.22	2814
HSA-MIR-12131	99.48	68.72	1673
HSA-MIR-1275	99.47	67.90	2749
HSA-MIR-7151-3P	99.04	69.72	2370
HSA-MIR-6749-3P	99.00	65.73	1443
HSA-MIR-4717-5P	98.19	67.97	894
HSA-MIR-4665-5P	97.91	67.69	1536
HSA-MIR-500A-3P	97.60	67.48	595
HSA-MIR-4639-3P	97.54	67.12	787
HSA-MIR-509-3-5P	97.21	67.74	1517
HSA-MIR-509-5P	97.21	67.90	1512
HSA-MIR-4418	97.04	67.16	1372

Literature-anchored findings (GeneRIF, showing 3)

• FOXP4 and SHROOM1 genes are hypermethylated in the knee osteoarthritic cartilage. (PMID:26484395)
• These data provide molecular insight into the Shroom-Rock interface and demonstrate that Shroom directly participates in regulating cytoskeletal dynamics, adding to its known role in Rock localization. (PMID:27758857)
• Suppression of SHROOM1 Improves In Vitro and In Vivo Gene Integration by Promoting Homology-Directed Repair. (PMID:32823670)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	shroom1	ENSDARG00000094181
mus_musculus	Shroom1	ENSMUSG00000018387
rattus_norvegicus	Shroom1	ENSRNOG00000007431
drosophila_melanogaster	Shrm	FBGN0085408

Paralogs (3): SHROOM3 (ENSG00000138771), SHROOM2 (ENSG00000146950), SHROOM4 (ENSG00000158352)

Protein

Protein identifiers

Protein Shroom1 — Q2M3G4 (reviewed: Q2M3G4)

Alternative names: Apical protein 2

All UniProt accessions (3): A6NN40, C9JXU1, Q2M3G4

UniProt curated annotations — full annotation on UniProt →

Function. May be involved in the assembly of microtubule arrays during cell elongation.

Subunit / interactions. Interacts with F-actin.

Subcellular location. Cytoplasm. Cytoskeleton.

Domain organisation. The ASD1 domain mediates F-actin binding.

Similarity. Belongs to the shroom family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q2M3G4-1	1	yes
Q2M3G4-2	2

RefSeq proteins (3): NP_001166171, NP_001397708, NP_597713 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR014799	ASD2_dom	Domain
IPR014800	ASD1_dom	Domain
IPR027685	Shroom_fam	Family

Pfam: PF08687, PF08688

UniProt features (27 total): modified residue 8, region of interest 7, compositionally biased region 6, domain 2, chain 1, splice variant 1, sequence variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q2M3G4-F1	54.36	0.14

Functional residue map

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

Post-translational modifications (8): 1, 18, 103, 133, 137, 166, 190, 224

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 83 (showing top): GSE37336_LY6C_POS_VS_NEG_NAIVE_CD4_TCELL_DN, GOBP_ACTIN_FILAMENT_BUNDLE_ORGANIZATION, GGGTGGRR_PAX4_03, SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM4, BILD_E2F3_ONCOGENIC_SIGNATURE, GOBP_ACTIN_FILAMENT_ORGANIZATION, TGANTCA_AP1_C, GOCC_APICAL_PLASMA_MEMBRANE, RYTTCCTG_ETS2_B, GOMF_ACTIN_BINDING, GOCC_CELL_CELL_JUNCTION, NERF_Q2, GOCC_APICAL_PART_OF_CELL, chr5q31, MARSON_BOUND_BY_FOXP3_UNSTIMULATED

GO Biological Process (2): cell morphogenesis (GO:0000902), actin filament bundle assembly (GO:0051017)

GO Molecular Function (3): myosin II binding (GO:0045159), actin filament binding (GO:0051015), actin binding (GO:0003779)

GO Cellular Component (7): microtubule (GO:0005874), adherens junction (GO:0005912), apical plasma membrane (GO:0016324), cortical actin cytoskeleton (GO:0030864), apical junction complex (GO:0043296), cytoplasm (GO:0005737), cytoskeleton (GO:0005856)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cell-cell junction	2
anatomical structure morphogenesis	1
cellular component assembly	1
actin filament bundle organization	1
myosin binding	1
actin binding	1
protein-containing complex binding	1
cytoskeletal protein binding	1
microtubule cytoskeleton	1
polymeric cytoskeletal fiber	1
apical part of cell	1
plasma membrane region	1
actin cytoskeleton	1
cortical cytoskeleton	1
intracellular anatomical structure	1
cellular anatomical structure	1
intracellular membraneless organelle	1

Protein interactions and networks

STRING

548 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SHROOM1	MCAM	P43121	591
SHROOM1	SOWAHA	Q2M3V2	447
SHROOM1	CCNI2	Q6ZMN8	435
SHROOM1	SHROOM4	Q9ULL8	429
SHROOM1	SHROOM3	Q8TF72	417
SHROOM1	PRSS48	Q7RTY5	417
SHROOM1	GRXCR2	A6NFK2	407
SHROOM1	VSIG10L	Q86VR7	404
SHROOM1	WDR97	A6NE52	401
SHROOM1	SHROOM2	Q13796	401
SHROOM1	SOCS2	O14508	397
SHROOM1	TEX15	Q9BXT5	394
SHROOM1	ZNF837	Q96EG3	393
SHROOM1	SLC36A3	Q495N2	389
SHROOM1	PM20D1	Q6GTS8	375

IntAct

26 interactions, top by confidence:

A	B	Type	Score
YWHAH	PLEKHG3	psi-mi:“MI:0914”(association)	0.610
YWHAQ	IGLC7	psi-mi:“MI:0914”(association)	0.530
BAG2	HGS	psi-mi:“MI:0914”(association)	0.530
HSPA2	DNAJC13	psi-mi:“MI:0914”(association)	0.530
YWHAB	PLEKHG3	psi-mi:“MI:0914”(association)	0.480
YWHAQ	PLEKHG3	psi-mi:“MI:0914”(association)	0.480
SHROOM1	SFN	psi-mi:“MI:0915”(physical association)	0.400
Xpo1	IFT56	psi-mi:“MI:0914”(association)	0.350
YWHAB	PLEKHG3	psi-mi:“MI:0914”(association)	0.350
YWHAG	C1orf226	psi-mi:“MI:0914”(association)	0.350
YWHAB	FOXO6	psi-mi:“MI:0914”(association)	0.350
YWHAG	FOXO6	psi-mi:“MI:0914”(association)	0.350
YWHAQ	FOXO6	psi-mi:“MI:0914”(association)	0.350
YWHAH	FOXO6	psi-mi:“MI:0914”(association)	0.350
DUSP16	MEIOC	psi-mi:“MI:0914”(association)	0.350
NYX	POTEF	psi-mi:“MI:0914”(association)	0.350
HSPA2	HGS	psi-mi:“MI:0914”(association)	0.350
CREB3L2	PLEKHG3	psi-mi:“MI:0914”(association)	0.350
HSPA8	PLEKHG3	psi-mi:“MI:0914”(association)	0.350
P4HA3	ARHGAP10	psi-mi:“MI:0914”(association)	0.350
POMGNT2	FAM83G	psi-mi:“MI:0914”(association)	0.350
SLC1A3	DDX11L8	psi-mi:“MI:0914”(association)	0.350
SLC7A9	CDC7	psi-mi:“MI:0914”(association)	0.350
rsgA	SHROOM1	psi-mi:“MI:0915”(physical association)	0.000
SHROOM1	mclA	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (24): SHROOM1 (Affinity Capture-MS), SHROOM1 (Biochemical Activity), SHROOM1 (Affinity Capture-MS), SHROOM1 (Affinity Capture-MS), SHROOM1 (Affinity Capture-MS), SHROOM1 (Proximity Label-MS), MCAM (Reconstituted Complex), MCAM (Affinity Capture-Western), MCAM (FRET), SHROOM1 (Affinity Capture-MS), SHROOM1 (Proximity Label-MS), SHROOM1 (Proximity Label-MS), SHROOM1 (Proximity Label-MS), SHROOM1 (Affinity Capture-MS), SHROOM1 (Affinity Capture-MS)

ESM2 similar proteins: A0A0U1RQ45, A0A0U1RQS6, A0A286YF58, A0A2R8YCJ5, A0A7I2V3R4, A2A699, A2VDX9, A6NCS6, A6NGB7, A6NJG2, A6NKF7, A6NKL6, A6NLJ0, A8MVW0, B2RU40, B7Z1M9, B8ZZ34, C9JH25, C9JVW0, D4A9R4, J3QNX5, M0QZC1, P03971, P0CG09, P0DPE3, Q0PHV7, Q0VD38, Q14761, Q29RK8, Q29RM6, Q2KJ18, Q2M3G4, Q2M3V2, Q5T442, Q64697, Q69YZ2, Q6F5E0, Q6NY19, Q6UXK2, Q80XF7

Diamond homologs: A1Z9P3, A1ZA47, A2ALU4, A8E0R9, D4A702, E9Q9W7, O00151, O14910, O70209, O70400, O75112, O88952, P36202, P50479, P52944, P70271, P97879, Q01613, Q09JY9, Q0P5E6, Q0P5F3, Q13424, Q13796, Q27IV2, Q28626, Q2M3G4, Q32LM6, Q3SYZ8, Q3T005, Q3T0C8, Q53GG5, Q5E9E1, Q5F425, Q5RAA5, Q5RBI7, Q5SX79, Q61234, Q62920, Q66HS7, Q6AYD6

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 31 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Activation of BAD and translocation to mitochondria	5	181.3×	2e-09
Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex	5	159.9×	3e-09
SARS-CoV-1 targets host intracellular signalling and regulatory pathways	5	159.9×	3e-09
Activation of BH3-only proteins	5	118.2×	1e-08
RHO GTPases activate PKNs	5	75.5×	1e-07
Intrinsic Pathway for Apoptosis	5	69.7×	1e-07
SARS-CoV-1-host interactions	5	41.8×	2e-06
Apoptosis	5	40.0×	2e-06

GO biological processes:

GO term	Partners	Fold	FDR
intracellular protein localization	5	21.8×	5e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	101
Likely benign	5
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

935 predictions. Top by Δscore:

Variant	Effect	Δscore
5:132823136:C:CT	acceptor_gain	1.0000
5:132823244:TTTTA:T	donor_loss	1.0000
5:132823245:TTTA:T	donor_loss	1.0000
5:132823246:TTA:T	donor_loss	1.0000
5:132823247:TACCT:T	donor_loss	1.0000
5:132823249:CC:C	donor_loss	1.0000
5:132823619:TCA:T	donor_loss	1.0000
5:132823620:CA:C	donor_loss	1.0000
5:132823621:A:AC	donor_gain	1.0000
5:132823622:C:CT	donor_gain	1.0000
5:132823622:CT:C	donor_gain	1.0000
5:132823622:CTTT:C	donor_gain	1.0000
5:132824294:C:CA	donor_gain	1.0000
5:132824418:CA:C	acceptor_gain	1.0000
5:132824420:C:CC	acceptor_gain	1.0000
5:132823129:CTTGA:C	acceptor_loss	0.9900
5:132823136:C:T	acceptor_gain	0.9900
5:132823138:C:CT	acceptor_gain	0.9900
5:132823249:CCTG:C	donor_gain	0.9900
5:132823519:CCAC:C	acceptor_gain	0.9900
5:132823520:CACC:C	acceptor_gain	0.9900
5:132823523:C:T	acceptor_loss	0.9900
5:132823524:T:G	acceptor_loss	0.9900
5:132823621:ACTTT:A	donor_gain	0.9900
5:132823622:CTT:C	donor_gain	0.9900
5:132823622:CTTTC:C	donor_gain	0.9900
5:132823625:T:A	donor_gain	0.9900
5:132823629:G:A	donor_gain	0.9900
5:132823765:C:CC	acceptor_gain	0.9900
5:132823766:T:C	acceptor_loss	0.9900

AlphaMissense

5388 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
5:132825667:G:C	F158L	0.995
5:132825667:G:T	F158L	0.995
5:132825669:A:G	F158L	0.995
5:132825668:A:C	F158C	0.986
5:132825668:A:G	F158S	0.986
5:132823361:G:C	F705L	0.982
5:132823361:G:T	F705L	0.982
5:132823363:A:G	F705L	0.982
5:132823066:C:A	K763N	0.981
5:132823066:C:G	K763N	0.981
5:132825663:G:T	R160S	0.981
5:132825694:C:A	Q149H	0.979
5:132825694:C:G	Q149H	0.979
5:132823090:C:A	Q755H	0.977
5:132823090:C:G	Q755H	0.977
5:132823370:G:C	F702L	0.976
5:132823370:G:T	F702L	0.976
5:132823372:A:G	F702L	0.976
5:132823362:A:G	F705S	0.974
5:132823080:C:G	A759P	0.972
5:132823100:A:G	L752P	0.968
5:132823371:A:G	F702S	0.966
5:132823070:A:G	L762P	0.964
5:132825669:A:T	F158I	0.963
5:132823312:G:T	R722S	0.961
5:132824686:G:C	F390L	0.961
5:132824686:G:T	F390L	0.961
5:132824688:A:G	F390L	0.961
5:132823049:C:G	R769P	0.960
5:132825720:A:C	Y141D	0.959

dbSNP variants (sampled 300 via entrez): RS1000078374 (5:132832614 T>C), RS1000432955 (5:132828499 C>T), RS1000732607 (5:132822859 G>A), RS1000888580 (5:132828755 T>G), RS1001186328 (5:132822585 G>A,C,T), RS1001831651 (5:132830920 C>T), RS1001947700 (5:132830599 G>A), RS1002730607 (5:132832546 G>A), RS1002741537 (5:132826095 A>G), RS1002814700 (5:132824403 G>A,C,T), RS1003202176 (5:132825671 G>A,C,T), RS1003504414 (5:132832179 G>C,T), RS1004238299 (5:132831293 G>A), RS1004402091 (5:132827409 G>A), RS1004640116 (5:132821959 G>A)

Disease associations

OMIM: gene MIM:611179 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST003590_4	Apolipoprotein A-IV levels	4.000000e-06
GCST008916_34	Asthma	2.000000e-09

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0007848	apolipoprotein A-IV measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

25 total (human), top 25 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression	2
aristolochic acid I	increases expression	1
TL8-506	affects cotreatment, increases expression	1
dicrotophos	increases expression	1
triphenyl phosphate	affects expression	1
pirinixic acid	affects binding, increases activity, increases expression	1
lead acetate	increases expression	1
11-nor-delta(9)-tetrahydrocannabinol-9-carboxylic acid	affects methylation, increases abundance	1
coumarin	affects phosphorylation	1
CGP 52608	increases reaction, affects binding	1
belinostat	decreases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Zoledronic Acid	increases expression	1
Benzo(a)pyrene	affects methylation	1
Caffeine	affects phosphorylation	1
Cannabinoids	affects methylation, increases abundance	1
Estradiol	affects cotreatment, increases expression	1
Lead	decreases expression	1
Plant Extracts	affects cotreatment, decreases expression	1
Poly I-C	affects cotreatment, increases expression	1
Quercetin	affects phosphorylation	1
Smoke	decreases expression	1
Tobacco Smoke Pollution	increases expression	1
Valproic Acid	decreases expression, increases methylation	1
Aflatoxin B1	decreases expression	1

Clinical trials (associated diseases)

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