STEAP1

STEAP family member 1, the group of Serine proteases|STEAP family

Basic information

Region (hg38): 7:90154456-90164829

Previous symbols: [ "STEAP" ]

Links

ENSG00000164647 ∙ NCBI:26872 ∙ OMIM:604415 ∙ HGNC:11378 ∙ Uniprot:Q9UHE8 ∙ 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 STEAP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the STEAP1 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			19			19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	0	1

Variants in STEAP1

This is a list of pathogenic ClinVar variants found in the STEAP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-90159864-G-A		not specified	Uncertain significance (Dec 28, 2022)
7-90160813-C-A		not specified	Uncertain significance (Oct 04, 2024)
7-90160827-G-A		not specified	Uncertain significance (Sep 06, 2023)
7-90160873-T-A		not specified	Uncertain significance (Apr 27, 2024)
7-90160886-G-C		not specified	Uncertain significance (Jun 02, 2023)
7-90160907-C-G		not specified	Uncertain significance (Dec 01, 2022)
7-90160931-T-C		not specified	Uncertain significance (Apr 06, 2024)
7-90161039-T-C		not specified	Uncertain significance (Aug 11, 2022)
7-90161126-G-C		not specified	Uncertain significance (Mar 05, 2024)
7-90161130-C-A		not specified	Uncertain significance (Jul 25, 2023)
7-90161133-T-C		not specified	Uncertain significance (Oct 05, 2021)
7-90161228-T-C		not specified	Uncertain significance (Aug 15, 2023)
7-90161237-G-A		not specified	Uncertain significance (Jul 20, 2022)
7-90161261-T-A		not specified	Uncertain significance (Apr 07, 2022)
7-90161270-A-G		not specified	Uncertain significance (Nov 10, 2024)
7-90161277-G-A		not specified	Uncertain significance (Feb 23, 2023)
7-90162028-A-G		not specified	Uncertain significance (Oct 12, 2024)
7-90164486-G-A		not specified	Uncertain significance (Jan 06, 2023)
7-90164518-C-T		STEAP1-related disorder	Benign (May 04, 2018)
7-90164531-G-A		not specified	Uncertain significance (Jan 23, 2023)
7-90164537-A-T		not specified	Uncertain significance (Jan 06, 2023)
7-90164553-T-C		not specified	Uncertain significance (Sep 27, 2021)
7-90164622-T-C		not specified	Uncertain significance (Jan 20, 2023)
7-90164679-A-G		not specified	Uncertain significance (Jul 11, 2023)
7-90164721-G-C		not specified	Likely benign (Oct 09, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
STEAP1	protein_coding	protein_coding	ENST00000297205	4	10455

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000527	0.678	125709	0	38	125747	0.000151

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.119	164	168	0.974	0.00000760	2224
Missense in Polyphen		53	63.215	0.8384		852
Synonymous	1.00	50	59.9	0.835	0.00000287	634
Loss of Function	1.03	10	14.2	0.705	6.87e-7	173

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000344	0.000344
Ashkenazi Jewish	0.00	0.00
East Asian	0.000272	0.000272
Finnish	0.0000958	0.0000924
European (Non-Finnish)	0.000133	0.000132
Middle Eastern	0.000272	0.000272
South Asian	0.000229	0.000196
Other	0.000163	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 (Consensus)

Recessive Scores

• pRec: 0.137

Intolerance Scores

• loftool: 0.556
• rvis_EVS: -0.21
• rvis_percentile_EVS: 38.58

Haploinsufficiency Scores

• pHI: 0.0581
• hipred: N
• hipred_score: 0.364
• ghis: 0.542

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.324

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Steap1

Gene ontology

• Biological process: ion transport;iron ion homeostasis;transmembrane transport;oxidation-reduction process
• Cellular component: endosome;plasma membrane;integral component of plasma membrane;cell-cell junction;endosome membrane;membrane
• Molecular function: transporter activity;channel activity;oxidoreductase activity;metal ion binding