OLFML1

olfactomedin like 1

Basic information

Region (hg38): 11:7485388-7511377

Links

ENSG00000183801 ∙ NCBI:283298 ∙ ∙ HGNC:24473 ∙ Uniprot:Q6UWY5 ∙ 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 OLFML1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OLFML1 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			21	1		22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	1	0

Variants in OLFML1

This is a list of pathogenic ClinVar variants found in the OLFML1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-7485916-T-G		not specified	Uncertain significance (Feb 16, 2023)
11-7485987-C-A		not specified	Uncertain significance (Feb 17, 2024)
11-7488154-A-G		not specified	Uncertain significance (Sep 16, 2021)
11-7488277-C-A		not specified	Uncertain significance (Feb 22, 2023)
11-7488296-A-T		not specified	Uncertain significance (Feb 05, 2024)
11-7488325-G-A		not specified	Uncertain significance (Apr 29, 2024)
11-7488362-T-C		not specified	Uncertain significance (May 26, 2024)
11-7488398-G-A		not specified	Uncertain significance (Jul 26, 2022)
11-7509478-G-T		not specified	Uncertain significance (Dec 28, 2022)
11-7509514-A-T		not specified	Uncertain significance (Jan 30, 2024)
11-7509560-C-T		not specified	Uncertain significance (Dec 20, 2023)
11-7509662-A-G		not specified	Uncertain significance (Mar 02, 2023)
11-7509670-G-A		not specified	Uncertain significance (May 25, 2022)
11-7509674-C-T		not specified	Uncertain significance (Dec 09, 2023)
11-7509757-T-A		not specified	Uncertain significance (Jan 09, 2024)
11-7509784-T-A		not specified	Uncertain significance (Apr 01, 2022)
11-7509788-T-C		not specified	Uncertain significance (Feb 06, 2024)
11-7509827-A-G		not specified	Uncertain significance (Oct 21, 2021)
11-7509842-C-G		not specified	Uncertain significance (Jun 16, 2023)
11-7509875-C-T		not specified	Uncertain significance (Mar 16, 2022)
11-7509905-A-G		not specified	Uncertain significance (Jun 18, 2024)
11-7509973-A-G		not specified	Uncertain significance (Dec 08, 2021)
11-7510081-C-T		not specified	Uncertain significance (Apr 07, 2023)
11-7510117-C-G		not specified	Uncertain significance (May 02, 2024)
11-7510134-A-C		not specified	Likely benign (Aug 08, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OLFML1	protein_coding	protein_coding	ENST00000329293	3	25990

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.59e-8	0.395	125628	2	118	125748	0.000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.693	249	220	1.13	0.0000110	2622
Missense in Polyphen		87	76.027	1.1443		910
Synonymous	0.559	77	83.5	0.922	0.00000411	791
Loss of Function	0.824	14	17.7	0.789	0.00000110	190

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00180	0.00180
Ashkenazi Jewish	0.00	0.00
East Asian	0.00136	0.00136
Finnish	0.00	0.00
European (Non-Finnish)	0.000274	0.000273
Middle Eastern	0.00136	0.00136
South Asian	0.000949	0.000882
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.222
• rvis_EVS: 1.15
• rvis_percentile_EVS: 92.56

Haploinsufficiency Scores

• pHI: 0.305
• hipred: N
• hipred_score: 0.247
• ghis: 0.489

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.272

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Olfml1

Gene ontology

• Cellular component: extracellular region