DOC2A

double C2 domain alpha, the group of Synaptotagmin like tandem C2 proteins

Basic information

Region (hg38): 16:30005514-30023270

Links

ENSG00000149927 ∙ NCBI:8448 ∙ OMIM:604567 ∙ HGNC:2985 ∙ Uniprot:Q14183 ∙ 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 DOC2A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DOC2A 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			36	1	3	40
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding				1		1
Total	0	0	36	2	3

Variants in DOC2A

This is a list of pathogenic ClinVar variants found in the DOC2A region.

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

Position	Type	Phenotype	Significance	ClinVar
16-30006206-C-T		not specified	Uncertain significance (Nov 30, 2022)
16-30006215-G-C			Benign (Dec 31, 2019)
16-30006257-C-T		not specified	Likely benign (Nov 13, 2024)
16-30006262-G-A			Benign (Jul 29, 2018)
16-30006286-T-C		not specified	Uncertain significance (Apr 26, 2023)
16-30006293-G-A		not specified	Uncertain significance (Feb 08, 2025)
16-30006298-T-G		not specified	Uncertain significance (Aug 20, 2024)
16-30006299-C-T		not specified	Uncertain significance (Nov 10, 2022)
16-30006419-A-G		not specified	Uncertain significance (Dec 02, 2024)
16-30006427-G-A		not specified	Uncertain significance (Feb 06, 2025)
16-30006493-A-G		not specified	Uncertain significance (Sep 11, 2024)
16-30006497-C-T		not specified	Uncertain significance (Aug 14, 2024)
16-30006621-T-G		not specified	Uncertain significance (Jan 29, 2025)
16-30006638-C-G		not specified	Uncertain significance (Jul 22, 2024)
16-30006664-C-T		not specified	Uncertain significance (Sep 29, 2023)
16-30006685-TG-T			Likely benign (Dec 31, 2019)
16-30006812-T-C		not specified	Uncertain significance (Sep 04, 2024)
16-30006869-C-T		not specified	Uncertain significance (Feb 25, 2025)
16-30006870-G-A		not specified	Uncertain significance (Dec 01, 2022)
16-30006884-C-G		not specified	Uncertain significance (Aug 30, 2022)
16-30006900-T-G		not specified	Uncertain significance (Sep 20, 2024)
16-30006929-C-T		not specified	Uncertain significance (Jul 15, 2021)
16-30006938-G-A		not specified	Uncertain significance (Mar 04, 2025)
16-30006948-A-C		not specified	Uncertain significance (Mar 14, 2025)
16-30006952-C-T			Benign (Dec 31, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DOC2A	protein_coding	protein_coding	ENST00000350119	10	17762

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00670	0.990	125721	0	27	125748	0.000107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.09	210	259	0.810	0.0000177	2555
Missense in Polyphen		41	65.344	0.62745		736
Synonymous	-0.0847	118	117	1.01	0.00000879	818
Loss of Function	2.56	7	19.1	0.367	0.00000101	213

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000185	0.000185
Ashkenazi Jewish	0.000201	0.000198
East Asian	0.000435	0.000435
Finnish	0.0000932	0.0000924
European (Non-Finnish)	0.0000991	0.0000967
Middle Eastern	0.000435	0.000435
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Calcium sensor which most probably regulates fusion of vesicles with membranes. Binds calcium and phospholipids. May be involved in calcium dependent neurotransmitter release through the interaction with UNC13A. May be involved in calcium-dependent spontaneous release of neurotransmitter in absence of action potentials in neuronal cells. Regulates Ca(2+)-dependent secretory lysosome exocytosis in mast cells. {ECO:0000269|PubMed:18354201, ECO:0000269|PubMed:9736751, ECO:0000269|PubMed:9804756}.

Recessive Scores

• pRec: 0.110

Intolerance Scores

• loftool: 0.601
• rvis_EVS: -0.56
• rvis_percentile_EVS: 19.73

Haploinsufficiency Scores

• pHI: 0.297
• hipred: Y
• hipred_score: 0.552
• ghis: 0.582

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.554

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Doc2a
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Zebrafish Information Network

• Gene name: doc2a
• Affected structure: ventricular system
• Phenotype tag: abnormal
• Phenotype quality: decreased size

Gene ontology

• Biological process: chemical synaptic transmission;nervous system development;synaptic vesicle exocytosis;regulation of calcium ion-dependent exocytosis
• Cellular component: nucleus;nucleolus;lysosome;cell junction;neuron projection;extrinsic component of synaptic vesicle membrane
• Molecular function: calcium ion binding;protein binding;calcium-dependent phospholipid binding