CLEC17A

C-type lectin domain containing 17A, the group of C-type lectin domain containing

Basic information

Region (hg38): 19:14583084-14612035

Links

ENSG00000187912 ∙ NCBI:388512 ∙ OMIM:616838 ∙ HGNC:34520 ∙ Uniprot:Q6ZS10 ∙ 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 CLEC17A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CLEC17A 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			25	2		27
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	2	0

Variants in CLEC17A

This is a list of pathogenic ClinVar variants found in the CLEC17A region.

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

Position	Type	Phenotype	Significance	ClinVar
19-14583167-A-G		not specified	Uncertain significance (Jul 09, 2021)
19-14583198-C-T		not specified	Likely benign (Dec 19, 2023)
19-14587621-G-A		not specified	Uncertain significance (Dec 20, 2022)
19-14587621-G-T		not specified	Uncertain significance (Feb 22, 2023)
19-14587676-C-A		not specified	Uncertain significance (Feb 27, 2024)
19-14587676-C-T		not specified	Uncertain significance (Jul 20, 2021)
19-14592301-G-A		not specified	Uncertain significance (Nov 09, 2023)
19-14592303-G-T		not specified	Likely benign (Aug 02, 2021)
19-14592314-A-G		not specified	Uncertain significance (Jan 25, 2023)
19-14592316-G-A		not specified	Uncertain significance (Dec 28, 2022)
19-14592331-C-G		not specified	Uncertain significance (Dec 22, 2023)
19-14594662-G-T		not specified	Uncertain significance (Jan 11, 2023)
19-14594667-C-A		not specified	Uncertain significance (Jan 23, 2023)
19-14595281-T-A		not specified	Uncertain significance (May 31, 2023)
19-14595309-C-G		not specified	Uncertain significance (Dec 06, 2022)
19-14596938-A-T		not specified	Uncertain significance (Jun 29, 2023)
19-14597113-G-C		not specified	Uncertain significance (Nov 08, 2022)
19-14600036-C-T		not specified	Uncertain significance (Dec 27, 2023)
19-14600037-G-A		not specified	Uncertain significance (Dec 13, 2021)
19-14600037-G-C		not specified	Uncertain significance (Sep 16, 2021)
19-14600058-G-C		not specified	Uncertain significance (Sep 06, 2022)
19-14600061-G-C		not specified	Uncertain significance (Oct 02, 2023)
19-14600074-G-C		not specified	Uncertain significance (Jul 06, 2021)
19-14600123-C-T		not specified	Uncertain significance (Jul 12, 2023)
19-14607050-A-G		not specified	Uncertain significance (Mar 19, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CLEC17A	protein_coding	protein_coding	ENST00000417570	14	28074

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.10e-8	0.921	124080	6	554	124640	0.00225

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.880	162	197	0.823	0.0000100	2457
Missense in Polyphen		35	56.281	0.62188		763
Synonymous	1.80	50	69.0	0.725	0.00000332	679
Loss of Function	1.79	15	24.6	0.611	0.00000131	286

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0149	0.0149
Ashkenazi Jewish	0.000109	0.0000994
East Asian	0.00219	0.00212
Finnish	0.000697	0.000696
European (Non-Finnish)	0.0000624	0.0000619
Middle Eastern	0.00219	0.00212
South Asian	0.0000662	0.0000654
Other	0.00102	0.000992

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Cell surface receptor which may be involved in carbohydrate-mediated communication between cells in the germinal center. Binds glycans with terminal alpha-linked mannose or fucose residues. {ECO:0000269|PubMed:19419970}.

Intolerance Scores

• loftool: 0.695
• rvis_EVS: 0.13
• rvis_percentile_EVS: 63

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.198
• ghis: 0.539

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.138

Gene Damage Prediction

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

Gene ontology

• Cellular component: cell surface;integral component of membrane
• Molecular function: mannose binding;fucose binding;metal ion binding