OLFML3

olfactomedin like 3

Basic information

Region (hg38): 1:113979391-114035572

Links

ENSG00000116774 ∙ NCBI:56944 ∙ OMIM:610088 ∙ HGNC:24956 ∙ Uniprot:Q9NRN5 ∙ 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 OLFML3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OLFML3 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			25			25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	0	2

Variants in OLFML3

This is a list of pathogenic ClinVar variants found in the OLFML3 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-113979530-C-G		not specified	Uncertain significance (Mar 28, 2024)
1-113979530-C-T		not specified	Uncertain significance (Oct 17, 2023)
1-113979575-A-G		not specified	Uncertain significance (Feb 06, 2024)
1-113980365-C-T		not specified	Uncertain significance (Mar 18, 2024)
1-113980384-G-T		not specified	Uncertain significance (Dec 22, 2023)
1-113980410-C-G		not specified	Uncertain significance (Jan 27, 2022)
1-113980418-G-C		not specified	Uncertain significance (Oct 03, 2022)
1-113980482-C-T		not specified	Uncertain significance (Dec 26, 2023)
1-113980492-G-A		not specified	Uncertain significance (Jan 16, 2024)
1-113980498-T-C		not specified	Uncertain significance (Dec 14, 2023)
1-113980504-A-G		not specified	Uncertain significance (Apr 07, 2023)
1-113980612-T-C		not specified	Uncertain significance (Dec 13, 2021)
1-113980950-C-G		Malignant tumor of prostate	Uncertain significance (-)
1-113980960-A-C		not specified	Uncertain significance (Jun 11, 2024)
1-113980963-A-G		not specified	Uncertain significance (Dec 16, 2023)
1-113981108-G-A		not specified	Uncertain significance (Dec 19, 2023)
1-113981133-C-A		EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)
1-113981134-C-G		not specified	Uncertain significance (Jul 05, 2022)
1-113981134-C-T		not specified	Uncertain significance (May 02, 2023)
1-113981191-T-G		not specified	Uncertain significance (Aug 12, 2022)
1-113981216-G-A		not specified	Uncertain significance (Jan 22, 2024)
1-113981294-G-C		not specified	Uncertain significance (Jun 01, 2023)
1-113981341-C-G		not specified	Uncertain significance (Jan 04, 2024)
1-113981416-C-T		not specified	Uncertain significance (Aug 18, 2023)
1-113981477-A-G		not specified	Uncertain significance (Oct 03, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OLFML3	protein_coding	protein_coding	ENST00000320334	3	2814

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.62e-8	0.423	125675	0	73	125748	0.000290

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.190	235	243	0.966	0.0000141	2597
Missense in Polyphen		84	94.827	0.88582		975
Synonymous	1.31	76	92.0	0.826	0.00000462	864
Loss of Function	0.805	13	16.5	0.786	0.00000104	169

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000177	0.000177
Ashkenazi Jewish	0.00	0.00
East Asian	0.000872	0.000870
Finnish	0.0000950	0.0000924
European (Non-Finnish)	0.000276	0.000273
Middle Eastern	0.000872	0.000870
South Asian	0.000538	0.000523
Other	0.000497	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Secreted scaffold protein that plays an essential role in dorsoventral patterning during early development. Stabilizes axial formation by restricting chordin (CHRD) activity on the dorsal side. Acts by facilitating the association between the tolloid proteases and their substrate chordin (CHRD), leading to enhance chordin (CHRD) degradation (By similarity). May have matrix-related function involved in placental and embryonic development, or play a similar role in other physiological processes. {ECO:0000250, ECO:0000269|PubMed:15280020}.

Recessive Scores

• pRec: 0.110

Intolerance Scores

• loftool: 0.321
• rvis_EVS: 0.06
• rvis_percentile_EVS: 58.85

Haploinsufficiency Scores

• pHI: 0.669
• hipred: N
• hipred_score: 0.282
• ghis: 0.559

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.966

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Olfml3
• Phenotype: normal phenotype

Gene ontology

• Biological process: multicellular organism development
• Cellular component: extracellular vesicle