OLFM1

olfactomedin 1

Basic information

Region (hg38): 9:135075422-135121180

Links

ENSG00000130558 ∙ NCBI:10439 ∙ OMIM:605366 ∙ HGNC:17187 ∙ Uniprot:Q99784 ∙ 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 OLFM1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OLFM1 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					3	3
missense			8			8
nonsense						0
start loss						0
frameshift				1	1	2
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	1	4

Variants in OLFM1

This is a list of pathogenic ClinVar variants found in the OLFM1 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-135077048-GA-G			Benign (Jul 01, 2022)
9-135077150-GCA-G			Likely benign (Nov 01, 2023)
9-135095885-A-T		not specified	Uncertain significance (Dec 27, 2023)
9-135098306-T-G		not specified	Uncertain significance (Mar 30, 2024)
9-135106789-C-T			Benign (Dec 31, 2019)
9-135106794-C-A		not specified	Uncertain significance (Nov 17, 2023)
9-135106834-C-T			Benign (Jun 19, 2018)
9-135119543-C-T		not specified	Uncertain significance (Mar 21, 2024)
9-135119594-C-T		not specified	Uncertain significance (Mar 28, 2024)
9-135119598-G-A		not specified	Uncertain significance (Oct 06, 2021)
9-135119662-G-A			Benign (Jul 31, 2018)
9-135119716-G-T		not specified	Uncertain significance (Mar 07, 2024)
9-135119720-C-T		not specified	Uncertain significance (Jul 14, 2021)
9-135119721-G-A		not specified	Uncertain significance (Jan 23, 2024)
9-135119979-G-C		not specified	Uncertain significance (Jun 16, 2024)
9-135120012-A-G		not specified	Uncertain significance (Jul 25, 2023)
9-135120155-G-A		not specified	Uncertain significance (Sep 01, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OLFM1	protein_coding	protein_coding	ENST00000252854	6	45758

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.997	0.00321	125735	0	4	125739	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.41	131	296	0.442	0.0000184	3102
Missense in Polyphen		41	104.32	0.39302		948
Synonymous	0.580	122	130	0.935	0.00000970	862
Loss of Function	4.08	1	21.3	0.0469	9.08e-7	236

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)	0.0000353	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Contributes to the regulation of axonal growth in the embryonic and adult central nervous system by inhibiting interactions between RTN4R and LINGO1. Inhibits RTN4R-mediated axon growth cone collapse (By similarity). May play an important role in regulating the production of neural crest cells by the neural tube (By similarity). May be required for normal responses to olfactory stimuli (By similarity). {ECO:0000250|UniProtKB:O88998, ECO:0000250|UniProtKB:Q9IAK4}.

Recessive Scores

• pRec: 0.257

Intolerance Scores

• loftool: 0.219
• rvis_EVS: -0.6
• rvis_percentile_EVS: 17.75

Haploinsufficiency Scores

• pHI: 0.748
• hipred: Y
• hipred_score: 0.809
• ghis: 0.672

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.681

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Olfm1
• Phenotype: reproductive system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); homeostasis/metabolism phenotype

Zebrafish Information Network

• Gene name: olfm1a
• Affected structure: retinal ganglion cell
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: atrioventricular valve formation;nervous system development;positive regulation of gene expression;negative regulation of gene expression;positive regulation of epithelial to mesenchymal transition;neuronal signal transduction;regulation of axon extension;cardiac epithelial to mesenchymal transition
• Cellular component: extracellular space;cell;endoplasmic reticulum;cell junction;axon;neuronal cell body;perikaryon;axonal growth cone;synapse
• Molecular function: protein binding