STEAP2

STEAP2 metalloreductase, the group of STEAP family

Basic information

Region (hg38): 7:90167590-90238137

Previous symbols: [ "PCANAP1" ]

Links

ENSG00000157214 ∙ NCBI:261729 ∙ OMIM:605094 ∙ HGNC:17885 ∙ Uniprot:Q8NFT2 ∙ 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 STEAP2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the STEAP2 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			29	2	1	32
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	29	3	1

Variants in STEAP2

This is a list of pathogenic ClinVar variants found in the STEAP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-90225078-G-A		STEAP2-related disorder	Likely benign (Sep 13, 2019)
7-90225089-T-C		not specified	Uncertain significance (Oct 17, 2024)
7-90225092-A-G		not specified	Uncertain significance (Jan 02, 2024)
7-90225098-A-G		not specified	Uncertain significance (Oct 02, 2023)
7-90225108-G-A		not specified	Uncertain significance (Sep 17, 2021)
7-90225138-C-T		not specified	Uncertain significance (Oct 09, 2024)
7-90225155-A-G		not specified	Uncertain significance (Sep 10, 2024)
7-90225195-G-A		not specified	Uncertain significance (Nov 14, 2023)
7-90225200-G-A		not specified	Uncertain significance (Jan 17, 2023)
7-90225239-G-A		not specified	Uncertain significance (Jun 05, 2023)
7-90225240-G-T		not specified	Uncertain significance (Oct 03, 2022)
7-90225243-A-G		not specified	Uncertain significance (Feb 14, 2023)
7-90225301-G-T		STEAP2-related disorder	Likely benign (Aug 02, 2020)
7-90225315-A-G		not specified	Uncertain significance (May 10, 2024)
7-90225341-A-T		not specified	Uncertain significance (Apr 25, 2022)
7-90225344-A-G		not specified	Uncertain significance (Jun 28, 2024)
7-90225497-G-T		not specified	Uncertain significance (Aug 13, 2021)
7-90225539-G-A		not specified	Uncertain significance (May 04, 2023)
7-90225546-A-G		not specified	Uncertain significance (Nov 21, 2024)
7-90225569-C-T		not specified	Uncertain significance (Jan 03, 2024)
7-90225570-G-A		not specified	Uncertain significance (Nov 10, 2024)
7-90226986-A-G		not specified	Uncertain significance (Feb 23, 2023)
7-90227139-A-G		STEAP2-related disorder	Likely benign (Aug 17, 2022)
7-90227189-T-G		not specified	Uncertain significance (Dec 19, 2022)
7-90227216-C-G		not specified	Uncertain significance (Jun 22, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
STEAP2	protein_coding	protein_coding	ENST00000287908	4	70548

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.25e-7	0.900	125607	0	134	125741	0.000533

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.753	223	257	0.868	0.0000123	3187
Missense in Polyphen		51	66.153	0.77094		839
Synonymous	2.22	64	91.0	0.703	0.00000436	963
Loss of Function	1.68	14	22.6	0.619	0.00000149	246

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000658	0.000656
Ashkenazi Jewish	0.000101	0.0000992
East Asian	0.000218	0.000217
Finnish	0.000278	0.000277
European (Non-Finnish)	0.000823	0.000818
Middle Eastern	0.000218	0.000217
South Asian	0.000394	0.000392
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Metalloreductase that has the ability to reduce both Fe(3+) to Fe(2+) and Cu(2+) to Cu(1+). Uses NAD(+) as acceptor (By similarity). {ECO:0000250}.
• Pathway: Mineral absorption - Homo sapiens (human);Copper homeostasis;Transferrin endocytosis and recycling;Transport of small molecules;Iron uptake and transport (Consensus)

Recessive Scores

• pRec: 0.107

Intolerance Scores

• loftool: 0.345
• rvis_EVS: 0.51
• rvis_percentile_EVS: 80.1

Haploinsufficiency Scores

• pHI: 0.0344
• hipred: N
• hipred_score: 0.393
• ghis: 0.445

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.140

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Steap2

Gene ontology

• Biological process: Golgi to plasma membrane transport;endocytosis;response to hormone;copper ion import;regulated exocytosis;iron ion homeostasis;oxidation-reduction process;iron ion import across cell outer membrane
• Cellular component: endosome;early endosome;cytosol;plasma membrane;endosome membrane;trans-Golgi network transport vesicle;integral component of Golgi membrane
• Molecular function: transporter activity;cupric reductase activity;metal ion binding;ferric-chelate reductase (NADPH) activity