ALLC

allantoicase

Basic information

Region (hg38): 2:3658200-3702671

Links

ENSG00000151360 ∙ NCBI:55821 ∙ OMIM:612396 ∙ HGNC:17377 ∙ Uniprot:Q8N6M5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ALLC gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ALLC gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			24	1	2	27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	24	1	2

Variants in ALLC

This is a list of pathogenic ClinVar variants found in the ALLC region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
2-3671176-T-A		not specified	Uncertain significance (Jan 17, 2023)
2-3671183-G-C		not specified	Uncertain significance (Aug 26, 2022)
2-3678478-C-A		not specified	Uncertain significance (Dec 20, 2023)
2-3678478-C-G		not specified	Uncertain significance (Aug 08, 2023)
2-3678480-T-C		not specified	Uncertain significance (Apr 04, 2023)
2-3679913-C-T		not specified	Uncertain significance (Nov 01, 2022)
2-3679916-G-A		not specified	Uncertain significance (Mar 30, 2024)
2-3679935-C-G		not specified	Uncertain significance (Jan 23, 2024)
2-3679980-C-A		not specified	Uncertain significance (Apr 22, 2022)
2-3681707-T-G		not specified	Uncertain significance (Jan 23, 2024)
2-3682999-C-G		not specified	Uncertain significance (Jan 05, 2022)
2-3683024-T-A		not specified	Uncertain significance (Mar 25, 2024)
2-3683030-A-G		not specified	Uncertain significance (Dec 14, 2022)
2-3695718-T-A		not specified	Uncertain significance (Nov 23, 2021)
2-3695747-G-T		not specified	Uncertain significance (Nov 17, 2023)
2-3695815-G-A		not specified	Uncertain significance (Jul 13, 2022)
2-3696328-G-T		not specified	Uncertain significance (Mar 22, 2023)
2-3696331-C-T		not specified	Uncertain significance (Oct 12, 2022)
2-3696332-G-A		not specified	Uncertain significance (Nov 10, 2022)
2-3696344-T-C		not specified	Uncertain significance (Aug 02, 2023)
2-3697356-G-C		not specified	Likely benign (Nov 29, 2023)
2-3697400-G-A			Benign (May 09, 2018)
2-3697410-T-A		not specified	Uncertain significance (Jan 30, 2024)
2-3701529-T-C			Benign (May 09, 2018)
2-3701599-C-T		not specified	Uncertain significance (Dec 23, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ALLC	protein_coding	protein_coding	ENST00000252505	11	44477

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.23e-16	0.00609	124294	1	376	124671	0.00151

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.196	214	222	0.963	0.0000127	2551
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00624	0.00622
Ashkenazi Jewish	0.00	0.00
East Asian	0.00128	0.00128
Finnish	0.000236	0.000232
European (Non-Finnish)	0.00142	0.00141
Middle Eastern	0.00128	0.00128
South Asian	0.00239	0.00236
Other	0.00116	0.00116

dbNSFP

Source: dbNSFP

• Function: FUNCTION: The function of this enzyme is unclear as allantoicase activity is not known to exist in mammals.
• Pathway: Purine metabolism - Homo sapiens (human);Purine nucleotides nucleosides metabolism (Consensus)

Recessive Scores

• pRec: 0.145

Intolerance Scores

• loftool: 0.419
• rvis_EVS: 1
• rvis_percentile_EVS: 90.69

Haploinsufficiency Scores

• pHI: 0.110
• hipred: N
• hipred_score: 0.275
• ghis: 0.396

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0227

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Allc

Gene ontology

• Biological process: allantoin catabolic process
• Molecular function: allantoicase activity