ALLC

protein-coding

allantoicase

Gene summary

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.[supplied by OMIM, Nov 2008]

MANE transcript

NM_018436.4

Inheritance

—

ClinVar variants

U:53B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.05

Max pathogenic AF

—

Genomic locus

chr2:3,658,200-3,702,671

External References & Databases

Ensembl (ENSG00000151360)

Transcript & Mutation Effects

hg38 • Region Span ~44.5 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ALLC variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 57

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_018436.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			53 clinvar	4 clinvar	2 clinvar	59
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	53	4	2	59

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 7 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_018436.4	RefSeq	NP_060906.3	11	MANE Select
ENST00000252505.4	Ensembl	ENSP00000252505.3	11	MANE Select
XM_011510369.3	RefSeq	XP_011508671.1	9	Standard
XM_017004495.2	RefSeq	XP_016859984.1	12	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Purine metabolism - Homo sapiens (human)
Purine nucleotides nucleosides metabolism

Biological Process

allantoin catabolic process

Molecular Function

allantoicase activity

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000252505
Coding exons: 11
Length: 44477
Individuals with no LoFs: 124294
Homozygous LoFs: 1
Heterozygous LoFs: 376
Defined: 124671
p: 0.00151

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.196	214	222	0.963	0.0000127	2551
Missense (PolyPhen)		65	72.868	0.89203		828
Synonymous	0.122	84	85.4	0.983	0.00000573	754
Loss of Function	-0.206	23	22.0	1.05	0.00000125	239

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0055	0.0054	notable
Latino/Admixed American	0.00078	0.00078	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.0013	0.0013	notable
Finnish	0.00024	0.00023	rare
European (Non-Finnish)	0.0014	0.0014	notable
South Asian	0.0024	0.0024	notable
Other	0.0012	0.0012	notable

dbNSFP Gene Annotations

Source: dbNSFP

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

Recessive Scores

pRec: 0.145

Intolerance Scores

LoFtool: 0.419
RVIS EVS: 1
RVIS percentile EVS: 90.69

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0227

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	Medium	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High