STEAP1

protein-coding

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

Gene summary

This gene is predominantly expressed in prostate tissue, and is found to be upregulated in multiple cancer cell lines. The gene product is predicted to be a six-transmembrane protein, and was shown to be a cell surface antigen significantly expressed at cell-cell junctions. [provided by RefSeq, Jul 2008]

Previous symbols:

STEAP

MANE transcript

NM_012449.3

Inheritance

—

ClinVar variants

U:54B:2

Top phenotype

STEAP1-related disorder

gnomAD constraint

pLI —, LoF o/e 0.7

Max pathogenic AF

—

Genomic locus

chr7:90,154,456-90,164,829

External References & Databases

Ensembl (ENSG00000164647)

Transcript & Mutation Effects

hg38 • Region Span ~10.4 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to STEAP1 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 52

not providedTotal: 1

STEAP1-related disorderTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_012449.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous					1 clinvar	1
missense			53 clinvar	1 clinvar		54
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	54	1	1	56

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 18 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_012449.3	RefSeq	NP_036581.1	4	MANE Select
ENST00000297205.7	Ensembl	ENSP00000297205.2	4	MANE Select
ENST00000412573.1	Ensembl	ENSP00000394402.1	3	Standard
ENST00000892309.1	Ensembl	ENSP00000562368.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Mineral absorption - Homo sapiens (human)
Copper homeostasis

Biological Process

ion transport
iron ion homeostasis
transmembrane transport
oxidation-reduction process

Molecular Function

transporter activity
channel activity
oxidoreductase activity
metal ion binding

Cellular Component

endosome
plasma membrane
integral component of plasma membrane
cell-cell junction
endosome membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000297205
Coding exons: 4
Length: 10455
Individuals with no LoFs: 125709
Homozygous LoFs: 0
Heterozygous LoFs: 38
Defined: 125747
p: 0.000151

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.119	164	168	0.974	0.00000760	2224
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.00022	0.00020	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00027	0.00027	rare
Finnish	0.000096	0.000092	rare
European (Non-Finnish)	0.00013	0.00013	rare
South Asian	0.00023	0.00020	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.137

Intolerance Scores

LoFtool: 0.556
RVIS EVS: -0.21
RVIS percentile EVS: 38.58

Essentials

Essential (CRISPR): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.324

Gene Damage Prediction

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