OLFM3

olfactomedin 3

Basic information

Region (hg38): 1:101802559-101996926

Links

ENSG00000118733 ∙ NCBI:118427 ∙ OMIM:607567 ∙ HGNC:17990 ∙ Uniprot:Q96PB7 ∙ 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 OLFM3 gene.

• Inborn genetic diseases (12 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OLFM3 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				2		2
missense			12			12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	2	0

Variants in OLFM3

This is a list of pathogenic ClinVar variants found in the OLFM3 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-101804245-T-C		not specified	Uncertain significance (May 04, 2022)
1-101804276-T-C		not specified	Uncertain significance (Jun 03, 2022)
1-101804360-A-G		not specified	Uncertain significance (Sep 06, 2022)
1-101804383-T-C		not specified	Uncertain significance (Nov 28, 2023)
1-101804544-A-T		not specified	Uncertain significance (Oct 05, 2021)
1-101804849-C-T		not specified	Uncertain significance (Nov 10, 2023)
1-101806082-G-T		not specified	Uncertain significance (Dec 18, 2023)
1-101825046-C-T		not specified	Uncertain significance (Jun 10, 2022)
1-101825080-G-A		not specified	Uncertain significance (Apr 18, 2023)
1-101825106-A-G		not specified	Uncertain significance (Aug 01, 2022)
1-101825116-G-C		not specified	Uncertain significance (Jan 30, 2024)
1-101825131-C-G		not specified	Uncertain significance (Sep 16, 2021)
1-101825188-T-C		not specified	Uncertain significance (Sep 01, 2021)
1-101825204-G-A			Likely benign (Apr 01, 2023)
1-101825242-A-C		not specified	Uncertain significance (Jun 16, 2023)
1-101830669-T-C		Strabismus, susceptibility to	Uncertain significance (Sep 01, 2020)
1-101836895-C-T		not specified	Uncertain significance (Jan 09, 2024)
1-101836954-G-A			Likely benign (Apr 01, 2023)
1-101836983-C-T		not specified	Uncertain significance (Feb 05, 2024)
1-101837024-G-C		not specified	Uncertain significance (Jan 12, 2024)
1-101996797-A-C		not specified	Uncertain significance (Feb 17, 2024)
1-101996806-G-T		not specified	Uncertain significance (Aug 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OLFM3	protein_coding	protein_coding	ENST00000370103	6	194457

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00102	0.997	125733	0	15	125748	0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.61	174	245	0.710	0.0000120	3032
Missense in Polyphen		79	124.46	0.63474		1533
Synonymous	-2.05	115	90.2	1.27	0.00000432	844
Loss of Function	2.68	9	22.8	0.394	0.00000128	258

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000246	0.000246
Ashkenazi Jewish	0.0000996	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000708	0.0000703
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000328	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.122

Intolerance Scores

• loftool: 0.279
• rvis_EVS: -0.76
• rvis_percentile_EVS: 13.33

Haploinsufficiency Scores

• pHI: 0.259
• hipred: N
• hipred_score: 0.343
• ghis: 0.653

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.853

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Olfm3

Gene ontology

• Biological process: eye photoreceptor cell development
• Cellular component: extracellular space;Golgi apparatus;cell junction;AMPA glutamate receptor complex;synapse
• Molecular function: protein binding