OLFM4

olfactomedin 4

Basic information

Region (hg38): 13:53028813-53052057

Links

ENSG00000102837 ∙ NCBI:10562 ∙ OMIM:614061 ∙ HGNC:17190 ∙ Uniprot:Q6UX06 ∙ 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 OLFM4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OLFM4 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			22	1		23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	1	0

Variants in OLFM4

This is a list of pathogenic ClinVar variants found in the OLFM4 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-53028847-G-A		not specified	Uncertain significance (Oct 25, 2023)
13-53028900-T-G		not specified	Uncertain significance (Jun 06, 2023)
13-53028906-G-C		not specified	Uncertain significance (Aug 08, 2022)
13-53028957-G-C		not specified	Uncertain significance (Aug 26, 2022)
13-53028967-C-T		not specified	Uncertain significance (Feb 05, 2024)
13-53029009-G-A		not specified	Uncertain significance (May 15, 2024)
13-53034366-G-A		not specified	Uncertain significance (Jan 03, 2024)
13-53034435-A-G		not specified	Uncertain significance (Nov 12, 2021)
13-53034445-G-A		not specified	Uncertain significance (Sep 01, 2021)
13-53034463-A-G		not specified	Uncertain significance (Jul 02, 2024)
13-53034475-A-G		not specified	Uncertain significance (Jun 22, 2021)
13-53041952-C-G		not specified	Uncertain significance (Sep 09, 2024)
13-53041991-G-C		not specified	Uncertain significance (Jun 28, 2024)
13-53042006-A-G		not specified	Uncertain significance (Jan 26, 2023)
13-53043118-C-T		not specified	Uncertain significance (Jun 17, 2024)
13-53043156-A-C		not specified	Uncertain significance (Sep 14, 2021)
13-53043250-C-T		not specified	Uncertain significance (Sep 16, 2021)
13-53050073-T-C		not specified	Uncertain significance (Jan 23, 2023)
13-53050074-C-T		not specified	Uncertain significance (Aug 10, 2021)
13-53050106-G-C		not specified	Uncertain significance (May 07, 2024)
13-53050181-T-C		not specified	Uncertain significance (Oct 08, 2024)
13-53050229-A-G		not specified	Uncertain significance (Mar 29, 2022)
13-53050263-T-C		not specified	Uncertain significance (Nov 08, 2024)
13-53050353-G-A		not specified	Uncertain significance (Dec 14, 2023)
13-53050482-T-C		not specified	Uncertain significance (Jan 03, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OLFM4	protein_coding	protein_coding	ENST00000219022	5	23299

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000278	0.774	122409	55	3284	125748	0.0134

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.342	264	280	0.942	0.0000150	3350
Missense in Polyphen		79	92.166	0.85715		1157
Synonymous	-0.523	119	112	1.06	0.00000622	1009
Loss of Function	1.26	11	16.5	0.665	8.53e-7	215

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00831	0.00831
Ashkenazi Jewish	0.00517	0.00517
East Asian	0.000440	0.000435
Finnish	0.0577	0.0575
European (Non-Finnish)	0.0151	0.0150
Middle Eastern	0.000440	0.000435
South Asian	0.00161	0.00160
Other	0.0137	0.0138

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May promote proliferation of pancreatic cancer cells by favoring the transition from the S to G2/M phase. In myeloid leukemic cell lines, inhibits cell growth and induces cell differentiation and apoptosis. May play a role in the inhibition of EIF4EBP1 phosphorylation/deactivation. Facilitates cell adhesion, most probably through interaction with cell surface lectins and cadherin. {ECO:0000269|PubMed:16566923, ECO:0000269|PubMed:17270022, ECO:0000269|PubMed:20724538}.
• Pathway: Neutrophil degranulation;Innate Immune System;Immune System (Consensus)

Recessive Scores

• pRec: 0.104

Intolerance Scores

• loftool: 0.246
• rvis_EVS: 0.53
• rvis_percentile_EVS: 80.96

Haploinsufficiency Scores

• pHI: 0.312
• hipred: N
• hipred_score: 0.146

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.262

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Olfm4
• Phenotype: immune system phenotype; digestive/alimentary phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: cell adhesion;regulation of necrotic cell death;regulation of apoptotic process;neutrophil degranulation;regulation of phagocytosis;protein homooligomerization;positive regulation of substrate adhesion-dependent cell spreading;regulation of neutrophil extravasation
• Cellular component: extracellular region;extracellular space;mitochondrion;plasma membrane;secretory granule;specific granule lumen;specific granule;azurophil granule;perinuclear region of cytoplasm;extracellular exosome;tertiary granule lumen
• Molecular function: catalytic activity;protein binding;protein homodimerization activity;cadherin binding