CLEC16A

C-type lectin domain containing 16A, the group of C-type lectin domain containing

Basic information

Region (hg38): 16:10944538-11182186

Previous symbols: [ "KIAA0350" ]

Links

ENSG00000038532 ∙ NCBI:23274 ∙ OMIM:611303 ∙ HGNC:29013 ∙ Uniprot:Q2KHT3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• schizophrenia (No Known Disease Relationship), mode of inheritance: Unknown

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CLEC16A gene.

• Inborn genetic diseases (43 variants)
• not provided (10 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CLEC16A 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				5		5
missense			42	5	1	48
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	42	10	1

Variants in CLEC16A

This is a list of pathogenic ClinVar variants found in the CLEC16A region.

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

Position	Type	Phenotype	Significance	ClinVar
16-10944763-A-G		not specified	Uncertain significance (Nov 18, 2022)
16-10957794-C-T			Likely benign (Apr 01, 2022)
16-10957834-A-C		not specified	Uncertain significance (Dec 19, 2023)
16-10962469-A-G		not specified	Uncertain significance (Feb 27, 2023)
16-10972945-C-A		not specified	Uncertain significance (Dec 08, 2023)
16-10972946-C-G		not specified	Uncertain significance (Jan 17, 2024)
16-10972947-A-C		not specified	Uncertain significance (Oct 12, 2021)
16-10977253-C-G		not specified	Uncertain significance (Dec 02, 2022)
16-10977290-A-G		not specified	Uncertain significance (Dec 17, 2023)
16-10977307-A-C		not specified	Uncertain significance (Dec 28, 2022)
16-10977331-C-T		not specified	Uncertain significance (Sep 26, 2023)
16-10979333-G-A		not specified	Uncertain significance (May 23, 2023)
16-10982881-T-G		not specified	Uncertain significance (Oct 12, 2021)
16-10982902-C-A			Uncertain significance (Oct 01, 2022)
16-10982971-C-G		not specified	Uncertain significance (Dec 17, 2021)
16-11003075-C-T		not specified	Uncertain significance (Mar 12, 2024)
16-11003090-G-A		not specified	Uncertain significance (Aug 10, 2023)
16-11003114-C-T		not specified	Uncertain significance (Jul 19, 2022)
16-11003123-G-A		not specified	Uncertain significance (Jan 11, 2023)
16-11003159-G-A		not specified	Uncertain significance (Apr 24, 2023)
16-11003289-G-A			Likely benign (Apr 10, 2018)
16-11003298-G-A			Benign/Likely benign (Apr 01, 2022)
16-11020210-A-G		not specified	Uncertain significance (Nov 18, 2023)
16-11020219-A-G		not specified	Uncertain significance (Dec 12, 2023)
16-11020241-C-G		not specified	Uncertain significance (Oct 24, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CLEC16A	protein_coding	protein_coding	ENST00000409790	24	237702

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.276	0.724	124949	0	24	124973	0.0000960

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.21	549	635	0.864	0.0000396	6887
Missense in Polyphen		129	188.8	0.68325		2077
Synonymous	-2.16	322	276	1.16	0.0000197	2035
Loss of Function	4.91	11	47.5	0.232	0.00000236	579

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000217	0.000213
Ashkenazi Jewish	0.00	0.00
East Asian	0.000170	0.000167
Finnish	0.000146	0.000139
European (Non-Finnish)	0.000109	0.000106
Middle Eastern	0.000170	0.000167
South Asian	0.0000330	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Regulator of mitophagy through the upstream regulation of the RNF41/NRDP1-PRKN pathway. Mitophagy is a selective form of autophagy necessary for mitochondrial quality control. The RNF41/NRDP1-PRKN pathway regulates autophagosome-lysosome fusion during late mitophagy. May protect RNF41/NRDP1 from proteosomal degradation, RNF41/NRDP1 which regulates proteosomal degradation of PRKN. Plays a key role in beta cells functions by regulating mitophagy/autophagy and mitochondrial health. {ECO:0000269|PubMed:24949970}.
• Pathway: Vitamin D Receptor Pathway (Consensus)

Recessive Scores

• pRec: 0.178

Intolerance Scores

• loftool: 0.775
• rvis_EVS: -1.01
• rvis_percentile_EVS: 8.2

Haploinsufficiency Scores

• pHI: 0.335
• hipred: Y
• hipred_score: 0.605
• ghis: 0.578

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.547

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Clec16a
• Phenotype: homeostasis/metabolism phenotype; cellular phenotype; growth/size/body region phenotype; endocrine/exocrine gland phenotype; hearing/vestibular/ear phenotype; limbs/digits/tail phenotype; vision/eye 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)

Gene ontology

• Biological process: autophagy;endosome to lysosome transport;cellular response to starvation;endosomal transport;negative regulation of proteasomal ubiquitin-dependent protein catabolic process;negative regulation of autophagosome maturation;positive regulation of autophagosome maturation;negative regulation of mitophagy;positive regulation of TORC1 signaling;negative regulation of macroautophagy by TORC1 signaling
• Cellular component: late endosome;Golgi apparatus;cytosol;integral component of membrane;vesicle;endolysosome membrane
• Molecular function: molecular_function;Rab GTPase binding