CLEC12A

C-type lectin domain family 12 member A, the group of CD molecules|C-type lectin domain containing

Basic information

Region (hg38): 12:9951316-9995694

Links

ENSG00000172322 ∙ NCBI:160364 ∙ OMIM:612088 ∙ HGNC:31713 ∙ Uniprot:Q5QGZ9 ∙ 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 CLEC12A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CLEC12A 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			15	1		16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	1	0

Variants in CLEC12A

This is a list of pathogenic ClinVar variants found in the CLEC12A region.

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

Position	Type	Phenotype	Significance	ClinVar
12-9971665-A-C		not specified	Uncertain significance (Sep 01, 2021)
12-9971669-G-A		not specified	Uncertain significance (Mar 19, 2024)
12-9978971-C-G		not specified	Uncertain significance (Nov 14, 2023)
12-9979411-T-G		not specified	Uncertain significance (Jun 11, 2024)
12-9979440-A-G		not specified	Uncertain significance (Jul 31, 2023)
12-9979447-A-G		not specified	Uncertain significance (Apr 11, 2023)
12-9979460-C-A		not specified	Uncertain significance (Mar 07, 2023)
12-9979515-A-G		not specified	Uncertain significance (Apr 22, 2024)
12-9980636-A-G		not specified	Uncertain significance (Sep 13, 2023)
12-9980654-T-G		not specified	Uncertain significance (Aug 09, 2021)
12-9980689-G-A		not specified	Uncertain significance (Jun 26, 2023)
12-9980699-C-A		not specified	Uncertain significance (Jan 24, 2024)
12-9980699-C-T		not specified	Uncertain significance (Jan 03, 2024)
12-9980721-C-G		not specified	Uncertain significance (Mar 31, 2024)
12-9980728-G-T		not specified	Uncertain significance (Jun 29, 2022)
12-9982058-G-C		not specified	Uncertain significance (Jun 06, 2023)
12-9982067-A-T		not specified	Uncertain significance (Feb 17, 2024)
12-9982082-T-A		not specified	Uncertain significance (Apr 24, 2023)
12-9982096-T-C		not specified	Uncertain significance (Aug 21, 2023)
12-9985009-T-C		not specified	Likely benign (Feb 28, 2023)
12-9993168-A-T		not specified	Uncertain significance (Nov 17, 2022)
12-9993258-T-A		not specified	Uncertain significance (Feb 23, 2023)
12-9993267-C-G		not specified	Uncertain significance (Oct 27, 2023)
12-9995176-C-G		not specified	Uncertain significance (May 27, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CLEC12A	protein_coding	protein_coding	ENST00000355690	7	44379

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.60e-7	0.304	125218	1	382	125601	0.00153

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.217	141	134	1.05	0.00000617	1827
Missense in Polyphen		36	38.791	0.92806		575
Synonymous	-0.234	46	44.0	1.04	0.00000197	465
Loss of Function	0.441	11	12.7	0.866	5.35e-7	168

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00153	0.00153
Ashkenazi Jewish	0.00270	0.00268
East Asian	0.000603	0.000598
Finnish	0.000140	0.000139
European (Non-Finnish)	0.00217	0.00215
Middle Eastern	0.000603	0.000598
South Asian	0.00132	0.00131
Other	0.00184	0.00180

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Cell surface receptor that modulates signaling cascades and mediates tyrosine phosphorylation of target MAP kinases. {ECO:0000269|PubMed:14739280, ECO:0000269|PubMed:16239426}.
• Pathway: Neutrophil degranulation;Innate Immune System;Immune System (Consensus)

Recessive Scores

• pRec: 0.128

Intolerance Scores

• loftool: 0.819
• rvis_EVS: 0.19
• rvis_percentile_EVS: 67.03

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.112
• ghis: 0.440

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0925

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Clec12a
• Phenotype: cellular phenotype; immune system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hematopoietic system phenotype

Gene ontology

• Biological process: neutrophil degranulation
• Cellular component: plasma membrane;integral component of membrane;specific granule membrane;tertiary granule membrane
• Molecular function: carbohydrate binding