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.

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.

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			9	1	1	11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding			5	2	9	16
Total	0	0	14	3	10

Variants in APIP

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

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

Position	Type	Phenotype	Significance	ClinVar
11-34882730-T-C		not specified	Uncertain significance (Aug 13, 2021)
11-34882782-C-T		not specified	Likely benign (Jun 10, 2024)
11-34883403-C-T		not specified	Uncertain significance (Aug 14, 2023)
11-34883493-A-G		not specified	Uncertain significance (Jan 29, 2024)
11-34888280-GAA-G			Benign (Jan 17, 2024)
11-34888286-A-AC			Likely benign (Jan 17, 2024)
11-34888378-G-C		not specified	Uncertain significance (Dec 06, 2022)
11-34888769-T-C		not specified	Uncertain significance (Mar 01, 2023)
11-34890511-C-T		not specified	Uncertain significance (Jul 14, 2021)
11-34890514-T-G		not specified	Uncertain significance (Nov 23, 2021)
11-34890551-C-T		not specified	Likely benign (Dec 27, 2023)
11-34895029-C-G		not specified	Uncertain significance (Mar 28, 2022)
11-34915816-C-T			Benign (Jun 14, 2018)
11-34915869-G-A			Benign (Jun 14, 2018)
11-34915939-G-C			Benign (Jun 14, 2018)
11-34916054-A-T			Benign (Jun 23, 2018)
11-34916137-C-A		Pyruvate dehydrogenase E3-binding protein deficiency	Likely benign (Jan 12, 2018)
11-34916150-T-C		Pyruvate dehydrogenase E3-binding protein deficiency	Benign (Jun 23, 2018)
11-34916151-G-A		Pyruvate dehydrogenase E3-binding protein deficiency	Benign (Jun 14, 2018)
11-34916171-G-C		Pyruvate dehydrogenase E3-binding protein deficiency	Uncertain significance (Jan 15, 2018)
11-34916259-C-G		not specified	Uncertain significance (Jan 03, 2024)
11-34916266-G-A		Pyruvate dehydrogenase E3-binding protein deficiency	Benign (Jun 23, 2018)
11-34916285-G-A		Pyruvate dehydrogenase E3-binding protein deficiency	Uncertain significance (Jan 13, 2018)
11-34916298-G-A		Pyruvate dehydrogenase E3-binding protein deficiency	Uncertain significance (Jan 12, 2018)
11-34916302-C-T		Pyruvate dehydrogenase E3-binding protein deficiency	Uncertain significance (Jan 12, 2018)

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-&alpha;-D-ribose 1-phosphate degradation;<i>S</i>-methyl-5-thio-&alpha;-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