STEAP4

STEAP4 metalloreductase, the group of STEAP family

Basic information

Region (hg38): 7:88270892-88306894

Previous symbols: [ "TNFAIP9" ]

Links

ENSG00000127954

∙ NCBI:79689 ∙ OMIM:611098 ∙ HGNC:21923 ∙ Uniprot:Q687X5 ∙ 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 STEAP4 gene.

not_specified (33 variants)
not_provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the STEAP4 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000024636.4. 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				1 clinvar		1
missense			31 clinvar	2 clinvar	2 clinvar	35
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	31	3	2

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
STEAP4	protein_coding	protein_coding	ENST00000380079	4	30463

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.20e-7	0.809	124512	2	273	124787	0.00110

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.843	208	245	0.848	0.0000123	2948
Missense in Polyphen		64	84.686	0.75573		1022
Synonymous	0.266	86	89.2	0.964	0.00000431	948
Loss of Function	1.45	14	21.2	0.659	0.00000145	221

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0135	0.0133
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000557	0.0000556
Finnish	0.0000464	0.0000464
European (Non-Finnish)	0.000284	0.000282
Middle Eastern	0.0000557	0.0000556
South Asian	0.000430	0.000425
Other	0.000664	0.000660

dbNSFP

Source: dbNSFP

Function: FUNCTION: Metalloreductase that has the ability to reduce both Fe(3+) to Fe(2+) and Cu(2+) to Cu(1+) (By similarity). Uses NADP(+) as acceptor (By similarity). Plays a role in systemic metabolic homeostasis, integrating inflammatory and metabolic responses (By similarity). Associated with obesity and insulin- resistance (PubMed:18430367, PubMed:18381574). Involved in inflammatory arthritis, through the regulation of inflammatory cytokines (PubMed:19660107). Inhibits anchorage-independent cell proliferation (PubMed:19787193). {ECO:0000250, ECO:0000269|PubMed:18381574, ECO:0000269|PubMed:18430367, ECO:0000269|PubMed:19660107, ECO:0000269|PubMed:19787193}.;
Pathway: Vitamin D Receptor Pathway;Copper homeostasis (Consensus)

Recessive Scores

pRec: 0.0817

Intolerance Scores

loftool: 0.524
rvis_EVS: 0.82
rvis_percentile_EVS: 87.95

Haploinsufficiency Scores

pHI: 0.102
hipred: N
hipred_score: 0.167
ghis: 0.422

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.375

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Steap4
Phenotype: adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); muscle phenotype; homeostasis/metabolism phenotype; immune system phenotype; cellular phenotype; liver/biliary system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); hematopoietic system phenotype;

Gene ontology

Biological process: copper ion import;fat cell differentiation;iron ion homeostasis;oxidation-reduction process;iron ion import across cell outer membrane
Cellular component: Golgi membrane;endosome;Golgi apparatus;plasma membrane;integral component of membrane;early endosome membrane;extracellular exosome
Molecular function: cupric reductase activity;metal ion binding;ferric-chelate reductase (NADPH) activity