CLEC14A

C-type lectin domain containing 14A, the group of C-type lectin domain containing

Basic information

Region (hg38): 14:38254000-38256093

Previous symbols: [ "C14orf27" ]

Links

ENSG00000176435 ∙ NCBI:161198 ∙ OMIM:616845 ∙ HGNC:19832 ∙ Uniprot:Q86T13 ∙ 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 CLEC14A gene.

• not_specified (71 variants)
• not_provided (2 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 CLEC14A gene is commonly pathogenic or not. These statistics are base on transcript: NM_000175060.3. 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					1	1
missense			70	2	1	73
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	70	2	2

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CLEC14A	protein_coding	protein_coding	ENST00000342213	1	2267

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000143	0.653	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.127	272	278	0.979	0.0000136	3093
Missense in Polyphen		83	87.254	0.95124		1004
Synonymous	-1.78	149	124	1.20	0.00000649	1093
Loss of Function	0.929	9	12.6	0.717	5.90e-7	124

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.439
• rvis_EVS: 0.33
• rvis_percentile_EVS: 73.54

Haploinsufficiency Scores

• pHI: 0.168
• hipred: N
• hipred_score: 0.247
• ghis: 0.475

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.113

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Clec14a
• Phenotype: normal phenotype

Zebrafish Information Network

• Gene name: clec14a
• Affected structure: epicardium
• Phenotype tag: abnormal
• Phenotype quality: increased size

Gene ontology

• Biological process: cell migration involved in sprouting angiogenesis;cell migration
• Cellular component: external side of plasma membrane;integral component of membrane;collagen-containing extracellular matrix
• Molecular function: carbohydrate binding;extracellular matrix binding;extracellular matrix protein binding