ALLC

Summary

ALLC (allantoicase, HGNC:17377) is a protein-coding gene on chromosome 2p25.3, encoding Probable inactive allantoicase (Q8N6M5). The function of this enzyme is unclear as allantoicase activity is not known to exist in mammals.

Allantoicase (EC 3.5.3.4) participates in the uric acid degradation pathway. Its enzymatic activity, like that of urate oxidase (MIM 191540), was lost during vertebrate evolution.

Source: NCBI Gene 55821 — RefSeq curated summary.

At a glance

• GWAS associations: 9
• Clinical variants (ClinVar): 68 total
• MANE Select transcript: NM_018436

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:17377
Approved symbol	ALLC
Name	allantoicase
Location	2p25.3
Locus type	gene with protein product
Status	Approved
Aliases	ALC
Ensembl gene	ENSG00000151360
Ensembl biotype	protein_coding
OMIM	612396
Entrez	55821

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 1 protein_coding, 1 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000252505, ENST00000471711, ENST00000476389

RefSeq mRNA: 1 — MANE Select: NM_018436 NM_018436

CCDS: CCDS46223

Canonical transcript exons

ENST00000252505 — 12 exons

Exon	Start	End
ENSE00000893309	3682942	3683074
ENSE00000893310	3681634	3681713
ENSE00000893311	3679869	3679994
ENSE00000893312	3678468	3678555
ENSE00001146000	3674075	3674125
ENSE00001189790	3671096	3671190
ENSE00001830659	3658200	3658294
ENSE00003521267	3701512	3701636
ENSE00003606448	3696275	3696348
ENSE00003627263	3697348	3697456
ENSE00003645787	3695717	3695872
ENSE00003666875	3702363	3702671

Expression profiles

Bgee: expression breadth ubiquitous, 139 present calls, max score 96.12.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0468 / max 47.8150, expressed in 6 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
18644	0.0401	6
202064	0.0067	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
sperm	CL:0000019	96.12	gold quality
male germ cell	CL:0000015	92.94	gold quality
right testis	UBERON:0004534	87.36	gold quality
left testis	UBERON:0004533	87.14	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	86.41	gold quality
testis	UBERON:0000473	84.15	gold quality
tibial nerve	UBERON:0001323	80.59	gold quality
right lobe of liver	UBERON:0001114	71.25	gold quality
adult organism	UBERON:0007023	68.72	gold quality
tongue squamous epithelium	UBERON:0006919	65.59	gold quality
gall bladder	UBERON:0002110	64.80	gold quality
dorsal root ganglion	UBERON:0000044	63.61	gold quality
choroid plexus epithelium	UBERON:0003911	63.05	gold quality
right adrenal gland cortex	UBERON:0035827	62.15	gold quality
trigeminal ganglion	UBERON:0001675	61.79	gold quality
liver	UBERON:0002107	61.67	gold quality
left adrenal gland cortex	UBERON:0035825	61.56	gold quality
diaphragm	UBERON:0001103	61.27	gold quality
right adrenal gland	UBERON:0001233	60.54	gold quality
left adrenal gland	UBERON:0001234	60.43	gold quality
sural nerve	UBERON:0015488	60.36	gold quality
adrenal cortex	UBERON:0001235	60.19	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	58.81	gold quality
gluteal muscle	UBERON:0002000	58.41	gold quality
superficial temporal artery	UBERON:0001614	58.27	gold quality
triceps brachii	UBERON:0001509	58.23	gold quality
adrenal gland	UBERON:0002369	57.50	gold quality
adult mammalian kidney	UBERON:0000082	57.13	gold quality
quadriceps femoris	UBERON:0001377	56.50	gold quality
parotid gland	UBERON:0001831	56.03	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	3.77

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

8 targeting ALLC, 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-3934-5P	99.67	64.04	846
HSA-MIR-12132	99.47	68.90	1341
HSA-MIR-4733-3P	98.35	65.20	994
HSA-MIR-4669	97.94	62.71	224
HSA-MIR-204-3P	97.80	66.84	1656
HSA-MIR-4646-5P	97.70	66.84	1692
HSA-MIR-10525-3P	96.32	68.04	699
HSA-MIR-6784-5P	84.56	60.91	126

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	allc	ENSDARG00000042562
mus_musculus	Allc	ENSMUSG00000020636
rattus_norvegicus	Dcdc2c	ENSRNOG00000008299

Protein

Protein identifiers

Probable inactive allantoicase — Q8N6M5 (reviewed: Q8N6M5)

Alternative names: Allantoate amidinohydrolase

All UniProt accessions (1): Q8N6M5

UniProt curated annotations — full annotation on UniProt →

Function. The function of this enzyme is unclear as allantoicase activity is not known to exist in mammals.

Polymorphism. Product of a polymorphic gene which also produces a longer 410-residue protein due to a polymorphism which affects Met-1, resulting in a longer protein starting at an upstream Met.

Similarity. Belongs to the allantoicase family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q8N6M5-1	1	yes
Q8N6M5-2	2

RefSeq proteins (1): NP_060906* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR005164	Allantoicase	Family
IPR008979	Galactose-bd-like_sf	Homologous_superfamily
IPR015908	Allantoicase_dom	Domain

Pfam: PF03561

UniProt features (6 total): sequence conflict 3, chain 1, splice variant 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8N6M5-F1	91.83	0.85

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 62 (showing top): chr2p25, GOBP_RESPONSE_TO_METAL_ION, GOBP_RESPONSE_TO_MAGNESIUM_ION, GOBP_AMIDE_METABOLIC_PROCESS, TGACATY_UNKNOWN, GOBP_RESPONSE_TO_ABIOTIC_STIMULUS, GOBP_RESPONSE_TO_PH, KEGG_PURINE_METABOLISM, SHEN_SMARCA2_TARGETS_DN, GOBP_RESPONSE_TO_CALCIUM_ION, GOMF_HYDROLASE_ACTIVITY_ACTING_ON_CARBON_NITROGEN_BUT_NOT_PEPTIDE_BONDS_IN_LINEAR_AMIDINES, GOMF_HYDROLASE_ACTIVITY_ACTING_ON_CARBON_NITROGEN_BUT_NOT_PEPTIDE_BONDS, ZWANG_TRANSIENTLY_UP_BY_2ND_EGF_PULSE_ONLY, ATF2_UP.V1_UP, NOTCH_DN.V1_DN

GO Biological Process (1): allantoin catabolic process (GO:0000256)

GO Molecular Function (1): allantoicase activity (GO:0004037)

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
allantoin metabolic process	1
catabolic process	1
hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines	1

Protein interactions and networks

STRING

901 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ALLC	MYC	P01106	742
ALLC	FOS	P01100	569
ALLC	EGFR	P00533	500
ALLC	DENND11	A4D1U4	454
ALLC	MPL	P40238	440
ALLC	AP1M1	Q9BXS5	430
ALLC	SRC	P12931	429
ALLC	SEC61A2	Q9H9S3	425
ALLC	PMFBP1	Q8TBY8	420
ALLC	KIT	P10721	419
ALLC	PCNX1	Q96RV3	418
ALLC	GTF3C5	Q9Y5Q8	416
ALLC	PREB	Q9HCU5	410
ALLC	COL9A1	P20849	401
ALLC	CLEC14A	Q86T13	393

IntAct

3 interactions, top by confidence:

A	B	Type	Score
GLI1	TP53	psi-mi:“MI:0914”(association)	0.350
NEK4	E2F8	psi-mi:“MI:0914”(association)	0.350

BioGRID (2): ALLC (Affinity Capture-MS), ALLC (Affinity Capture-MS)

ESM2 similar proteins: A1L1F0, A4IFG2, A5A6P1, A5GFY8, C3K0A7, D9IVE5, O43175, P10688, P10895, P18407, P25335, Q01415, Q02JZ8, Q09913, Q0V9A9, Q1ED21, Q2KIG4, Q32NH8, Q3B8C3, Q3KFK9, Q3TV70, Q48KS4, Q4K8H3, Q4R964, Q4ZVG8, Q58DU8, Q5EAD2, Q5PQR3, Q5R6J8, Q5R7M2, Q61753, Q640T1, Q68FH4, Q6AYP0, Q6DGA6, Q6LPX9, Q86WQ0, Q87YX4, Q8BIP0, Q8C726

Diamond homologs: A3MA02, A4VP32, A6V7Y9, B0V9T8, B0VP26, B2I1L5, B2UG65, B7GV54, B7ICG5, B7UW33, C3K0A7, P18407, P25335, Q02JZ8, Q09913, Q2KIG4, Q3KFK9, Q48KS4, Q4K8H3, Q4R964, Q4ZVG8, Q54VL5, Q5YP02, Q62H14, Q62JH0, Q63QS9, Q63T53, Q640T1, Q6AYP0, Q6DGA6, Q6F6Y1, Q6LPX9, Q82LL5, Q87YX4, Q8N6M5, Q8XUB7, Q92VC1, Q9I3J8, Q9JHX6, Q9RKU4

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	55
Likely benign	5
Benign	2

Top pathogenic / likely-pathogenic (0)

SpliceAI

2211 predictions. Top by Δscore:

Variant	Effect	Δscore
2:3671093:CA:C	acceptor_loss	1.0000
2:3671094:A:AG	acceptor_gain	1.0000
2:3671095:G:GG	acceptor_gain	1.0000
2:3671095:GGAA:G	acceptor_gain	1.0000
2:3671187:AAAAG:A	donor_loss	1.0000
2:3671188:AAAG:A	donor_loss	1.0000
2:3671190:AG:A	donor_loss	1.0000
2:3671191:G:GG	donor_gain	1.0000
2:3671191:GTA:G	donor_loss	1.0000
2:3671192:T:A	donor_loss	1.0000
2:3679864:C:CA	acceptor_gain	1.0000
2:3679864:CGCA:C	acceptor_loss	1.0000
2:3679865:GCAG:G	acceptor_loss	1.0000
2:3679866:CAG:C	acceptor_loss	1.0000
2:3679867:A:AG	acceptor_gain	1.0000
2:3679867:A:AT	acceptor_loss	1.0000
2:3679868:G:GT	acceptor_gain	1.0000
2:3679868:GGT:G	acceptor_gain	1.0000
2:3679868:GGTC:G	acceptor_gain	1.0000
2:3679988:G:GT	donor_gain	1.0000
2:3679991:GAAG:G	donor_gain	1.0000
2:3679992:AAGGT:A	donor_loss	1.0000
2:3679993:AGGT:A	donor_loss	1.0000
2:3679994:GGT:G	donor_loss	1.0000
2:3679995:G:GA	donor_loss	1.0000
2:3679996:T:G	donor_loss	1.0000
2:3695843:C:G	donor_gain	1.0000
2:3696346:G:GT	donor_gain	1.0000
2:3696346:GAA:G	donor_gain	1.0000
2:3696349:G:GG	donor_gain	1.0000

AlphaMissense

2579 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
2:3678528:T:A	W49R	0.983
2:3678528:T:C	W49R	0.983
2:3696307:T:A	W234R	0.980
2:3696307:T:C	W234R	0.980
2:3678530:G:C	W49C	0.972
2:3678530:G:T	W49C	0.972
2:3682957:T:A	W132R	0.971
2:3682957:T:C	W132R	0.971
2:3701610:T:A	W317R	0.966
2:3701610:T:C	W317R	0.966
2:3696309:G:C	W234C	0.965
2:3696309:G:T	W234C	0.965
2:3683058:A:C	R165S	0.957
2:3683058:A:T	R165S	0.957
2:3679967:T:C	S91P	0.954
2:3679971:T:A	I92N	0.954
2:3679880:T:C	C62R	0.953
2:3695741:T:A	V179E	0.950
2:3702480:G:C	G365R	0.948
2:3674081:T:C	F14L	0.947
2:3674083:T:A	F14L	0.947
2:3674083:T:G	F14L	0.947
2:3678529:G:C	W49S	0.945
2:3697390:G:C	A262P	0.945
2:3683057:G:C	R165T	0.943
2:3695833:T:C	F210L	0.942
2:3695835:T:A	F210L	0.942
2:3695835:T:G	F210L	0.942
2:3695836:A:C	S211R	0.942
2:3695838:T:A	S211R	0.942

dbSNP variants (sampled 300 via entrez): RS1000152971 (2:3686248 G>A), RS1000173483 (2:3674291 C>T), RS1000206276 (2:3674039 G>A), RS1000268034 (2:3649584 C>A), RS1000321712 (2:3679416 T>C), RS1000328552 (2:3692767 A>C), RS1000341228 (2:3668817 C>G,T), RS1000343297 (2:3674628 T>A,C), RS1000407967 (2:3659405 G>C), RS1000426667 (2:3679201 A>G), RS1000511255 (2:3663815 C>T), RS1000519692 (2:3669783 G>C), RS1000586849 (2:3654292 G>A), RS1000680951 (2:3652964 T>C), RS1000718792 (2:3669484 C>T)

Disease associations

OMIM: gene MIM:612396 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

9 associations (top):

Study	Trait	p-value
GCST001762_148	Obesity-related traits	2.000000e-06
GCST002432_1	Response to inhaled corticosteroid treatment in asthma (change in FEV1)	4.000000e-07
GCST002432_10	Response to inhaled corticosteroid treatment in asthma (change in FEV1)	4.000000e-06
GCST006312_1	Childhood dental caries in primary teeth	4.000000e-08
GCST006312_2	Childhood dental caries in primary teeth	4.000000e-07
GCST007565_23	Morning person	1.000000e-13
GCST007576_70	Chronotype	1.000000e-13
GCST008503_1	Fasting glucose change	1.000000e-06
GCST009286_1	Chronic kidney disease (reduced eGFR or end stage renal disease) in type 1 diabetes	9.000000e-09

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0005921	FEV change measurement
EFO:0008328	chronotype measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

13 total (human), top 13 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Aflatoxin B1	decreases methylation, increases methylation	2
sodium arsenite	affects methylation	1
butyraldehyde	increases expression	1
aflatoxin B2	increases methylation	1
CGP 52608	affects binding, increases reaction	1
abrine	increases expression	1
theaflavin-3,3’-digallate	affects expression	1
Arsenic	affects methylation	1
Benzo(a)pyrene	decreases methylation, affects methylation	1
Pesticides	affects methylation	1
Tetrachlorodibenzodioxin	increases expression	1
Urethane	decreases expression	1
Cyclosporine	increases expression	1

Clinical trials (associated diseases)

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