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.

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.

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				1		1
missense			22	2	2	26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	3	2

Variants in STEAP4

This is a list of pathogenic ClinVar variants found in the STEAP4 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-88279529-G-A		not specified	Uncertain significance (Aug 02, 2021)
7-88279546-T-A		not specified	Likely benign (Mar 01, 2023)
7-88279598-A-C		not specified	Uncertain significance (Feb 13, 2024)
7-88280924-T-A			Likely benign (Feb 01, 2018)
7-88281067-T-C		not specified	Uncertain significance (Jul 25, 2023)
7-88282649-C-T		not specified	Likely benign (Dec 09, 2023)
7-88282672-C-A			Benign (Jul 30, 2018)
7-88282795-C-T			Benign (Jul 16, 2018)
7-88282799-A-G		not specified	Uncertain significance (Oct 04, 2022)
7-88282810-C-T		not specified	Uncertain significance (Mar 24, 2023)
7-88282874-C-T		not specified	Uncertain significance (May 23, 2023)
7-88282910-C-T		not specified	Uncertain significance (Mar 19, 2024)
7-88282915-C-T		not specified	Uncertain significance (Jun 05, 2023)
7-88282927-T-G		not specified	Uncertain significance (Dec 14, 2021)
7-88283018-G-A		not specified	Uncertain significance (Oct 20, 2024)
7-88283030-T-C		not specified	Uncertain significance (Feb 28, 2024)
7-88283065-T-C		not specified	Uncertain significance (Oct 20, 2021)
7-88283084-C-G		not specified	Uncertain significance (Jul 27, 2021)
7-88283093-T-C		not specified	Uncertain significance (Jun 12, 2023)
7-88283159-A-G		not specified	Uncertain significance (Oct 08, 2024)
7-88283162-C-A		not specified	Uncertain significance (Apr 26, 2023)
7-88283818-C-T		not specified	Uncertain significance (May 31, 2024)
7-88283819-G-A		not specified	Uncertain significance (May 14, 2024)
7-88283896-A-G		not specified	Uncertain significance (Jul 02, 2024)
7-88283984-G-A		not specified	Uncertain significance (Dec 17, 2023)

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