STEAP1B

STEAP family member 1B, the group of STEAP family

Basic information

Region (hg38): 7:22419444-22727613

Links

ENSG00000105889 ∙ NCBI:256227 ∙ ∙ HGNC:41907 ∙ Uniprot:Q6NZ63 ∙ 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 STEAP1B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the STEAP1B 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						0
missense			9			9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	0	0

Variants in STEAP1B

This is a list of pathogenic ClinVar variants found in the STEAP1B region.

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

Position	Type	Phenotype	Significance	ClinVar
7-22492596-G-T		not specified	Uncertain significance (Dec 26, 2023)
7-22492605-A-G		not specified	Uncertain significance (Apr 09, 2024)
7-22492620-G-A		not specified	Uncertain significance (Nov 10, 2022)
7-22492671-T-A		not specified	Uncertain significance (Nov 10, 2022)
7-22492680-A-C		not specified	Uncertain significance (Dec 30, 2023)
7-22493335-C-T		not specified	Uncertain significance (Mar 25, 2024)
7-22493355-C-G		not specified	Uncertain significance (Mar 15, 2024)
7-22493579-G-C		not specified	Uncertain significance (Jun 13, 2024)
7-22493584-C-T		not specified	Uncertain significance (Dec 21, 2022)
7-22493589-A-G		not specified	Uncertain significance (Nov 09, 2022)
7-22493779-G-C		not specified	Uncertain significance (Sep 27, 2021)
7-22493824-C-T		not specified	Uncertain significance (Dec 02, 2022)
7-22493826-G-A		not specified	Uncertain significance (Apr 19, 2023)
7-22725249-C-A			Uncertain significance (-)
7-22726602-A-G		INTERLEUKIN 6 POLYMORPHISM	Benign (Mar 01, 2002)
7-22727026-C-G		Kaposi sarcoma • Crohn disease-associated growth failure, susceptibility to • • • Diabetes mellitus type 2, susceptibility to • Diabetes mellitus, type 1, susceptibility to • Cholangiocarcinoma	other; risk factor (Dec 10, 2022)
7-22727515-C-A		IL6-related disorder	Benign (Jun 12, 2018)
7-22727518-C-T			Benign (Dec 31, 2019)
7-22727543-C-A		not specified	Uncertain significance (Aug 13, 2021)
7-22727592-A-C		not specified	Likely benign (Mar 13, 2023)
7-22727607-C-T			Likely benign (Aug 23, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
STEAP1B	protein_coding	protein_coding	ENST00000404369	4	213482

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000124	0.621	125486	3	258	125747	0.00104

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.423	151	166	0.908	0.00000738	2228
Missense in Polyphen		58	63.553	0.91263		881
Synonymous	0.362	58	61.6	0.941	0.00000304	638
Loss of Function	0.870	9	12.3	0.732	6.07e-7	146

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0119	0.0118
Ashkenazi Jewish	0.000298	0.000298
East Asian	0.00120	0.00120
Finnish	0.0000466	0.0000462
European (Non-Finnish)	0.000169	0.000167
Middle Eastern	0.00120	0.00120
South Asian	0.000621	0.000621
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 1.84
• rvis_percentile_EVS: 97.06

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Gene ontology

• Cellular component: endosome;plasma membrane;integral component of membrane