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.

• not_specified (163 variants)
• EBV-positive_nodal_T-_and_NK-cell_lymphoma (1 variants)

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. These statistics are base on transcript: NM_000182487.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			156	8		164
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	156	8	0

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