CLEC16A

protein-coding

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

Gene summary

This gene encodes a member of the C-type lectin domain containing family. Single nucleotide polymorphisms in introns of this gene have been associated with diabetes mellitus, multiple sclerosis and rheumatoid arthritis. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2011]

Previous symbols:

KIAA0350

MANE transcript

NM_015226.3

Inheritance

—

ClinVar variants

U:169B:17

Top phenotype

Meniere disease

gnomAD constraint

pLI —, LoF o/e 0.23

Max pathogenic AF

—

Genomic locus

chr16:10,944,539-11,182,186

External References & Databases

Ensembl (ENSG00000038532)

Transcript & Mutation Effects

hg38 • Region Span ~237.6 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

schizophreniaNO_KNOWN

Inheritance Pattern: Unknown

Disease ID:MONDO:0005090

Submitter: Labcorp Genetics (formerly Invitae)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CLEC16A variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 157

not providedTotal: 11

Meniere diseaseTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_015226.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	7 clinvar		9
missense			156 clinvar	9 clinvar	1 clinvar	166
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			10 clinvar			10
Total	0	0	169	16	1	186

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 72 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_015226.3	RefSeq	NP_056041.1	24	MANE Select
ENST00000409790.6	Ensembl	ENSP00000387122.1	24	MANE Select
NM_001243403.2	RefSeq	NP_001230332.1	21	Standard
NM_001410905.1	RefSeq	NP_001397834.1	23	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Vitamin D Receptor Pathway

Biological Process

autophagy
endosome to lysosome transport
cellular response to starvation
endosomal transport
negative regulation of proteasomal ubiquitin-dependent protein catabolic process

Molecular Function

molecular_function
Rab GTPase binding

Cellular Component

late endosome
Golgi apparatus
cytosol
integral component of membrane
vesicle

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000409790
Coding exons: 24
Length: 237702
Individuals with no LoFs: 124949
Homozygous LoFs: 0
Heterozygous LoFs: 24
Defined: 124973
p: 0.0000960

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.21	549	635	0.864	0.0000396	6887
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00013	0.00013	rare
Latino/Admixed American	0.000087	0.000087	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00017	0.00017	rare
Finnish	0.00015	0.00014	rare
European (Non-Finnish)	0.00011	0.00011	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.178

Intolerance Scores

LoFtool: 0.775
RVIS EVS: -1.01
RVIS percentile EVS: 8.2

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.547

Gene Damage Prediction

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