CLEC1A

C-type lectin domain family 1 member A, the group of C-type lectin domain containing

Basic information

Region (hg38): 12:10069553-10111627

Links

ENSG00000150048 ∙ NCBI:51267 ∙ OMIM:606782 ∙ HGNC:24355 ∙ Uniprot:Q8NC01 ∙ 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 CLEC1A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CLEC1A 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			13	4	1	18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	4	1

Variants in CLEC1A

This is a list of pathogenic ClinVar variants found in the CLEC1A region.

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

Position	Type	Phenotype	Significance	ClinVar
12-10071349-A-G		not specified	Likely benign (Mar 11, 2022)
12-10071415-C-T		not specified	Uncertain significance (Aug 13, 2021)
12-10071484-G-A		not specified	Likely benign (May 03, 2023)
12-10073406-A-C		not specified	Uncertain significance (Nov 10, 2022)
12-10075566-A-T		not specified	Uncertain significance (Aug 09, 2021)
12-10081252-A-G		not specified	Uncertain significance (Sep 25, 2023)
12-10081360-C-G		not specified	Uncertain significance (Feb 17, 2022)
12-10089160-C-A		not specified	Uncertain significance (Aug 22, 2023)
12-10089160-C-T		not specified	Uncertain significance (Feb 16, 2023)
12-10089167-C-G		not specified	Uncertain significance (Jul 30, 2023)
12-10089183-A-G			Uncertain significance (-)
12-10089214-C-T		not specified	Likely benign (Feb 23, 2023)
12-10098828-T-C		not specified	Likely benign (Nov 07, 2022)
12-10098832-G-A		not specified	Uncertain significance (Sep 01, 2021)
12-10098846-C-G		Aspergillosis, susceptibility to	Benign (Apr 19, 2019)
12-10098871-T-C		not specified	Uncertain significance (Jan 31, 2022)
12-10098874-C-A		not specified	Uncertain significance (Dec 09, 2023)
12-10098893-G-C		not specified	Uncertain significance (Apr 13, 2022)
12-10098907-T-C		not specified	Uncertain significance (Apr 23, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CLEC1A	protein_coding	protein_coding	ENST00000315330	6	42074

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.63e-17	0.000319	125584	1	163	125748	0.000652

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.151	155	150	1.03	0.00000773	1839
Missense in Polyphen		23	23.338	0.98552		317
Synonymous	0.593	50	55.6	0.899	0.00000285	512
Loss of Function	-1.86	21	13.6	1.55	6.61e-7	154

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000723	0.000719
Ashkenazi Jewish	0.00764	0.00767
East Asian	0.000818	0.000816
Finnish	0.0000959	0.0000924
European (Non-Finnish)	0.000367	0.000352
Middle Eastern	0.000818	0.000816
South Asian	0.000327	0.000327
Other	0.000490	0.000489

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0754

Intolerance Scores

• loftool: 0.848
• rvis_EVS: 0.53
• rvis_percentile_EVS: 80.73

Haploinsufficiency Scores

• pHI: 0.0580
• hipred: N
• hipred_score: 0.123
• ghis: 0.388

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0462

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Clec1a

Gene ontology

• Biological process: defense response;cell surface receptor signaling pathway
• Cellular component: integral component of plasma membrane
• Molecular function: transmembrane signaling receptor activity;carbohydrate binding