OLFM2

olfactomedin 2

Basic information

Region (hg38): 19:9853718-9936515

Links

ENSG00000105088 ∙ NCBI:93145 ∙ OMIM:617492 ∙ HGNC:17189 ∙ Uniprot:O95897 ∙ 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 OLFM2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OLFM2 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					1	1
missense			21	2	2	25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding					8	8
Total	0	0	21	2	11

Variants in OLFM2

This is a list of pathogenic ClinVar variants found in the OLFM2 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-9854147-A-G			Benign (Nov 12, 2018)
19-9854204-G-T		not specified	Uncertain significance (Apr 07, 2023)
19-9854270-G-A			Benign (Jun 09, 2021)
19-9854302-T-C		not specified	Uncertain significance (Mar 29, 2023)
19-9854512-C-G		not specified	Uncertain significance (Dec 17, 2023)
19-9854515-C-T		not specified	Uncertain significance (Mar 25, 2024)
19-9854520-T-C		not specified	Uncertain significance (Apr 08, 2024)
19-9854629-C-T		not specified	Uncertain significance (Jul 14, 2021)
19-9854637-G-A		not specified	Uncertain significance (May 26, 2024)
19-9854665-G-A		not specified	Uncertain significance (Dec 08, 2023)
19-9854670-C-T		not specified	Uncertain significance (Mar 29, 2024)
19-9854692-C-T		not specified	Uncertain significance (Feb 12, 2024)
19-9854805-C-T		not specified	Uncertain significance (Feb 13, 2024)
19-9854830-G-A		not specified	Uncertain significance (May 25, 2022)
19-9854854-T-C		not specified	Uncertain significance (Nov 01, 2022)
19-9854869-G-A			Benign (Dec 31, 2019)
19-9855016-T-C			Benign (Jun 19, 2021)
19-9856753-C-T			Benign (Jun 20, 2021)
19-9856809-G-A		not specified	Uncertain significance (Aug 26, 2022)
19-9856817-G-A		not specified	Uncertain significance (Apr 18, 2023)
19-9856875-C-T		not specified	Likely benign (Dec 27, 2023)
19-9856896-C-T		not specified	Uncertain significance (Feb 15, 2023)
19-9857290-G-A		not specified	Uncertain significance (Mar 15, 2024)
19-9857442-G-C		not specified	Uncertain significance (Aug 28, 2023)
19-9857463-G-A			Benign (Jun 09, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OLFM2	protein_coding	protein_coding	ENST00000264833	6	82835

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0802	0.918	125738	0	10	125748	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.34	184	298	0.618	0.0000223	2930
Missense in Polyphen		64	122.41	0.52283		1193
Synonymous	0.604	125	134	0.934	0.0000107	920
Loss of Function	2.71	5	17.1	0.293	8.08e-7	189

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000557	0.0000544
Finnish	0.000102	0.0000924
European (Non-Finnish)	0.0000633	0.0000615
Middle Eastern	0.0000557	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in transforming growth factor beta (TGF-beta)- induced smooth muscle differentiation. TGF-beta induces expression and translocation of OLFM2 to the nucleus where it binds to SRF, causing its dissociation from the transcriptional repressor HEY2/HERP1 and facilitating binding of SRF to target genes (PubMed:25298399). Plays a role in AMPAR complex organization (By similarity). Is a regulator of vascular smooth-muscle cell (SMC) phenotypic switching, that acts by promoting RUNX2 and inhibiting MYOCD binding to SRF. SMC phenotypic switching is the process through which vascular SMCs undergo transition between a quiescent contractile phenotype and a proliferative synthetic phenotype in response to pathological stimuli. SMC phenotypic plasticity is essential for vascular development and remodeling (By similarity). {ECO:0000250|UniProtKB:Q568Y7, ECO:0000250|UniProtKB:Q8BM13, ECO:0000269|PubMed:25298399}.

Recessive Scores

• pRec: 0.128

Intolerance Scores

• loftool: 0.0594
• rvis_EVS: 0
• rvis_percentile_EVS: 53.73

Haploinsufficiency Scores

• pHI: 0.170
• hipred: Y
• hipred_score: 0.715
• ghis: 0.500

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.807

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Olfm2
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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); vision/eye phenotype

Zebrafish Information Network

• Gene name: olfm2a
• Affected structure: trigeminal motor nucleus
• Phenotype tag: abnormal
• Phenotype quality: fused with

Gene ontology

• Biological process: visual perception;locomotory behavior;protein secretion;positive regulation of smooth muscle cell differentiation;regulation of vascular smooth muscle cell dedifferentiation
• Cellular component: extracellular region;nucleus;nucleoplasm;cytoplasm;cell junction;AMPA glutamate receptor complex;glutamatergic synapse;extrinsic component of synaptic membrane
• Molecular function: protein binding