OLFML2A

olfactomedin like 2A

Basic information

Region (hg38): 9:124777133-124814885

Links

ENSG00000185585 ∙ NCBI:169611 ∙ OMIM:615899 ∙ HGNC:27270 ∙ Uniprot:Q68BL7 ∙ 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 OLFML2A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OLFML2A 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			69	4		73
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	69	4	0

Variants in OLFML2A

This is a list of pathogenic ClinVar variants found in the OLFML2A region.

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

Position	Type	Phenotype	Significance	ClinVar
9-124777290-C-A		not specified	Uncertain significance (May 31, 2023)
9-124786979-T-G		not specified	Uncertain significance (Dec 13, 2022)
9-124787027-G-A		not specified	Uncertain significance (Jan 10, 2023)
9-124787038-A-C		not specified	Uncertain significance (May 03, 2023)
9-124787045-G-A		not specified	Uncertain significance (Aug 16, 2022)
9-124787092-C-T		not specified	Uncertain significance (Apr 18, 2023)
9-124787174-T-C		not specified	Uncertain significance (Jun 28, 2022)
9-124787178-C-A		not specified	Uncertain significance (Apr 15, 2024)
9-124787179-C-T		not specified	Uncertain significance (Dec 20, 2023)
9-124787191-G-A		not specified	Uncertain significance (Jan 24, 2023)
9-124787193-G-C		not specified	Uncertain significance (Jun 09, 2022)
9-124787209-C-T		not specified	Uncertain significance (Apr 06, 2024)
9-124787216-A-G		not specified	Uncertain significance (Dec 20, 2023)
9-124795033-A-C		not specified	Uncertain significance (Dec 28, 2022)
9-124795087-G-A		not specified	Uncertain significance (Nov 30, 2022)
9-124799292-A-G		not specified	Likely benign (Feb 02, 2022)
9-124799306-C-T		not specified	Uncertain significance (May 20, 2024)
9-124799307-G-A		not specified	Uncertain significance (Jan 22, 2024)
9-124799336-C-G		not specified	Uncertain significance (Nov 22, 2023)
9-124799336-C-T		not specified	Uncertain significance (Apr 09, 2024)
9-124801582-G-A		not specified	Uncertain significance (May 13, 2024)
9-124801609-C-T		not specified	Uncertain significance (Jan 11, 2023)
9-124801610-G-A		not specified	Uncertain significance (Jul 13, 2021)
9-124801636-A-C		not specified	Uncertain significance (Jun 16, 2024)
9-124801651-G-C		not specified	Uncertain significance (Oct 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OLFML2A	protein_coding	protein_coding	ENST00000373580	8	37728

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.29e-9	0.795	125597	0	151	125748	0.000601

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.360	442	421	1.05	0.0000286	4217
Missense in Polyphen		108	107.33	1.0062		1060
Synonymous	0.721	178	191	0.934	0.0000142	1341
Loss of Function	1.58	18	26.8	0.672	0.00000138	297

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000561	0.000561
Ashkenazi Jewish	0.000198	0.000198
East Asian	0.000708	0.000707
Finnish	0.000370	0.000370
European (Non-Finnish)	0.000828	0.000827
Middle Eastern	0.000708	0.000707
South Asian	0.000425	0.000425
Other	0.000818	0.000815

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.197
• rvis_EVS: -0.73
• rvis_percentile_EVS: 14.2

Haploinsufficiency Scores

• pHI: 0.135
• hipred: N
• hipred_score: 0.197
• ghis: 0.539

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.945

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Olfml2a

Gene ontology

• Biological process: extracellular matrix organization
• Cellular component: extracellular matrix
• Molecular function: protein homodimerization activity;extracellular matrix binding