OR10Z1

olfactory receptor family 10 subfamily Z member 1, the group of Olfactory receptors, family 10

Basic information

Region (hg38): 1:158605267-158612514

Links

ENSG00000198967 ∙ NCBI:128368 ∙ ∙ HGNC:14996 ∙ Uniprot:Q8NGY1 ∙ 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 OR10Z1 gene.

• Pyropoikilocytosis, hereditary (28 variants)
• Hereditary spherocytosis type 3 (19 variants)
• Elliptocytosis 2 (19 variants)
• not provided (16 variants)
• Inborn genetic diseases (13 variants)
• Spherocytosis, Recessive (9 variants)
• Elliptocytosis (9 variants)
• not specified (1 variants)
• SPTA1-related condition (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OR10Z1 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			10	1		11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding		5	32	1	4	42
Total	0	5	42	2	4

Highest pathogenic variant AF is 0.0000132

Variants in OR10Z1

This is a list of pathogenic ClinVar variants found in the OR10Z1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-158606452-A-G		not specified	Uncertain significance (Mar 23, 2022)
1-158606454-G-A		not specified	Uncertain significance (Feb 16, 2023)
1-158606494-G-C		not specified	Uncertain significance (Aug 01, 2022)
1-158606504-G-T		not specified	Uncertain significance (Apr 13, 2022)
1-158606560-G-A		not specified	Uncertain significance (Dec 17, 2023)
1-158606944-G-T		not specified	Uncertain significance (Oct 05, 2023)
1-158606982-C-T		not specified	Uncertain significance (Jul 13, 2021)
1-158606983-C-T		not specified	Uncertain significance (Jul 13, 2021)
1-158607019-C-T		not specified	Likely benign (Jun 18, 2021)
1-158607053-G-T		not specified	Uncertain significance (Dec 05, 2022)
1-158607071-C-G		not specified	Uncertain significance (Sep 22, 2023)
1-158607148-C-T		not specified	Uncertain significance (Apr 13, 2023)
1-158607151-T-C		not specified	Uncertain significance (Apr 19, 2023)
1-158607162-G-T		not specified	Uncertain significance (Oct 05, 2023)
1-158607199-G-A		not specified	Uncertain significance (May 30, 2023)
1-158607210-G-A		not specified	Likely benign (Dec 11, 2023)
1-158607243-G-A		not specified	Uncertain significance (Dec 18, 2023)
1-158610755-C-A		Elliptocytosis 2 • Hereditary spherocytosis type 3 • Pyropoikilocytosis, hereditary	Uncertain significance (Jan 12, 2018)
1-158610763-TA-T		Elliptocytosis • Pyropoikilocytosis, hereditary • Spherocytosis, Recessive	Likely benign (Jun 14, 2016)
1-158610844-A-T		Elliptocytosis 2 • Hereditary spherocytosis type 3 • Pyropoikilocytosis, hereditary	Uncertain significance (Jan 13, 2018)
1-158610877-A-G		Pyropoikilocytosis, hereditary • Elliptocytosis 2 • Hereditary spherocytosis type 3	Conflicting classifications of pathogenicity (Jan 12, 2018)
1-158610885-C-T		Pyropoikilocytosis, hereditary • Hereditary spherocytosis type 3 • Elliptocytosis 2	Uncertain significance (Jan 13, 2018)
1-158610923-A-C		Pyropoikilocytosis, hereditary • Elliptocytosis 2 • Hereditary spherocytosis type 3	Uncertain significance (Jan 13, 2018)
1-158610941-A-G		Hereditary spherocytosis type 3 • Pyropoikilocytosis, hereditary • Elliptocytosis 2	Uncertain significance (Jan 13, 2018)
1-158610945-G-A		Pyropoikilocytosis, hereditary • Hereditary spherocytosis type 3 • Elliptocytosis 2	Uncertain significance (Jan 12, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OR10Z1	protein_coding	protein_coding	ENST00000361284	1	942

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.111	0.787	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.54	213	159	1.34	0.00000757	2034
Missense in Polyphen		92	72.217	1.2739		952
Synonymous	-1.93	88	67.8	1.30	0.00000355	678
Loss of Function	1.28	2	5.13	0.390	2.21e-7	75

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Odorant receptor. {ECO:0000305}.
• Pathway: Olfactory transduction - Homo sapiens (human);Olfactory receptor activity;Signaling by GPCR;Signal Transduction;Olfactory Signaling Pathway;G alpha (s) signalling events;GPCR downstream signalling (Consensus)

Intolerance Scores

• loftool: 0.639
• rvis_EVS: 0.73
• rvis_percentile_EVS: 86.17

Haploinsufficiency Scores

• pHI: 0.0996
• hipred: N
• hipred_score: 0.170

Essentials

• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.158

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Olfr419

Gene ontology

• Biological process: G protein-coupled receptor signaling pathway;detection of chemical stimulus involved in sensory perception of smell
• Cellular component: plasma membrane;integral component of membrane
• Molecular function: G protein-coupled receptor activity;olfactory receptor activity