DPPA3

developmental pluripotency associated 3

Basic information

Region (hg38): 12:7711433-7717559

Links

ENSG00000187569 ∙ NCBI:359787 ∙ OMIM:608408 ∙ HGNC:19199 ∙ Uniprot:Q6W0C5 ∙ 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 DPPA3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DPPA3 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			8	2		10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	2	0

Variants in DPPA3

This is a list of pathogenic ClinVar variants found in the DPPA3 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-7715203-G-A		not specified	Uncertain significance (Mar 15, 2024)
12-7715257-G-C		not specified	Uncertain significance (Dec 31, 2023)
12-7715261-C-T		not specified	Uncertain significance (Oct 26, 2021)
12-7715290-G-C		not specified	Likely benign (Jun 02, 2023)
12-7715291-A-C		not specified	Uncertain significance (May 23, 2024)
12-7715347-A-G		not specified	Uncertain significance (Jun 04, 2024)
12-7715384-A-G		not specified	Likely benign (Apr 25, 2023)
12-7715413-G-A		not specified	Uncertain significance (Jan 18, 2022)
12-7715414-G-A		not specified	Uncertain significance (May 16, 2023)
12-7717006-G-A		not specified	Uncertain significance (Apr 24, 2024)
12-7717018-T-C		not specified	Uncertain significance (Jun 21, 2022)
12-7717037-C-T		not specified	Uncertain significance (Feb 21, 2024)
12-7717049-A-G		not specified	Uncertain significance (Dec 15, 2022)
12-7717070-A-G		not specified	Uncertain significance (Oct 26, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DPPA3	protein_coding	protein_coding	ENST00000345088	4	6106

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.217	0.749	125484	0	3	125487	0.0000120

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.253	97	90.2	1.07	0.00000551	1021
Missense in Polyphen		19	17.528	1.084		230
Synonymous	0.0105	35	35.1	0.998	0.00000251	308
Loss of Function	1.76	2	7.05	0.284	3.69e-7	81

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000347	0.0000347
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000554	0.0000545
Finnish	0.00	0.00
European (Non-Finnish)	0.00000980	0.00000881
Middle Eastern	0.0000554	0.0000545
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Primordial germ cell (PGCs)-specific protein involved in epigenetic chromatin reprogramming in the zygote following fertilization. In zygotes, DNA demethylation occurs selectively in the paternal pronucleus before the first cell division, while the adjacent maternal pronucleus and certain paternally-imprinted loci are protected from this process. Participates in protection of DNA methylation in the maternal pronucleus by preventing conversion of 5mC to 5hmC: specifically recognizes and binds histone H3 dimethylated at 'Lys-9' (H3K9me2) on maternal genome, and protects maternal genome from TET3-mediated conversion to 5hmC and subsequent DNA demethylation. Does not bind paternal chromatin, which is mainly packed into protamine and does not contain much H3K9me2 mark. Also protects imprinted loci that are marked with H3K9me2 in mature sperm from DNA demethylation in early embryogenesis. May be important for the totipotent/pluripotent states continuing through preimplantation development. Also involved in chromatin condensation in oocytogenesis (By similarity). {ECO:0000250}.
• Pathway: Preimplantation Embryo (Consensus)

Recessive Scores

• pRec: 0.0723

Intolerance Scores

• loftool: 0.734
• rvis_EVS: 0.59
• rvis_percentile_EVS: 82.45

Haploinsufficiency Scores

• pHI: 0.0243
• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.221

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dppa3
• Phenotype: embryo 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); reproductive system phenotype; cellular phenotype

Gene ontology

• Biological process: chromatin organization;protection of DNA demethylation of female pronucleus;negative regulation of DNA demethylation;regulation of genetic imprinting
• Cellular component: female pronucleus;male pronucleus;nucleus;cytoplasm
• Molecular function: methylated histone binding