APIP

APAF1 interacting protein

Basic information

Region (hg38): 11:34853094-34916379

Links

ENSG00000149089

∙ NCBI:51074 ∙ OMIM:612491 ∙ HGNC:17581 ∙ Uniprot:Q96GX9 ∙ 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 APIP gene.

not_specified (25 variants)
not_provided (2 variants)
Pyruvate_dehydrogenase_E3-binding_protein_deficiency (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the APIP gene is commonly pathogenic or not. These statistics are base on transcript: NM_000015957.4. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			23 clinvar	2 clinvar		25
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	23	2	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
APIP	protein_coding	protein_coding	ENST00000395787	7	63406

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.69e-11	0.0216	125139	4	605	125748	0.00242

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.785	107	132	0.808	0.00000650	1568
Missense in Polyphen		29	35.91	0.80756		446
Synonymous	-0.0528	44	43.6	1.01	0.00000221	436
Loss of Function	-0.549	15	12.9	1.17	5.41e-7	174

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00162	0.00160
Ashkenazi Jewish	0.0134	0.0134
East Asian	0.00114	0.00109
Finnish	0.00200	0.00199
European (Non-Finnish)	0.00285	0.00283
Middle Eastern	0.00114	0.00109
South Asian	0.000934	0.000850
Other	0.00399	0.00392

dbNSFP

Source: dbNSFP

Function: FUNCTION: Catalyzes the dehydration of methylthioribulose-1- phosphate (MTRu-1-P) into 2,3-diketo-5-methylthiopentyl-1- phosphate (DK-MTP-1-P). Functions in the methionine salvage pathway, which plays a key role in cancer, apoptosis, microbial proliferation and inflammation. May inhibit the CASP1-related inflammatory response (pyroptosis), the CASP9-dependent apoptotic pathway and the cytochrome c-dependent and APAF1-mediated cell death. {ECO:0000255|HAMAP-Rule:MF_03116, ECO:0000269|PubMed:15262985, ECO:0000269|PubMed:22837397, ECO:0000269|PubMed:23285211, ECO:0000269|PubMed:24367089}.;
Pathway: Cysteine and methionine metabolism - Homo sapiens (human);Methionine De Novo and Salvage Pathway;Metabolism of polyamines;Metabolism of amino acids and derivatives;Methionine salvage pathway;Metabolism;<i>S</i>-methyl-5-thio-α-D-ribose 1-phosphate degradation;<i>S</i>-methyl-5-thio-α-D-ribose 1-phosphate degradation;methionine salvage cycle III;Sulfur amino acid metabolism (Consensus)

Recessive Scores

pRec: 0.120

Intolerance Scores

loftool: 0.884
rvis_EVS: 0.68
rvis_percentile_EVS: 85.04

Haploinsufficiency Scores

pHI: 0.209
hipred: N
hipred_score: 0.352
ghis: 0.441

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.370

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Apip
Phenotype: homeostasis/metabolism phenotype;

Gene ontology

Biological process: apoptotic process;L-methionine salvage from S-adenosylmethionine;L-methionine salvage from methylthioadenosine;negative regulation of apoptotic process;protein homotetramerization;pyroptosis;regulation of ERK1 and ERK2 cascade
Cellular component: cytoplasm
Molecular function: protein binding;zinc ion binding;identical protein binding;methylthioribulose 1-phosphate dehydratase activity