DPPA2

developmental pluripotency associated 2

Basic information

Region (hg38): 3:109293788-109316517

Links

ENSG00000163530 ∙ NCBI:151871 ∙ OMIM:614445 ∙ HGNC:19197 ∙ Uniprot:Q7Z7J5 ∙ 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 DPPA2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DPPA2 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		1	21	3	1	26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	1	21	3	1

Variants in DPPA2

This is a list of pathogenic ClinVar variants found in the DPPA2 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-109300423-C-T		not specified	Likely benign (Jul 23, 2024)
3-109304488-C-G		not specified	Uncertain significance (Sep 05, 2024)
3-109304496-A-G		Premature ovarian failure	Likely pathogenic (Mar 02, 2020)
3-109304523-G-T		not specified	Uncertain significance (Dec 31, 2024)
3-109304541-A-G		not specified	Uncertain significance (Mar 27, 2023)
3-109304592-C-A		not specified	Uncertain significance (Apr 17, 2024)
3-109304601-A-G		not specified	Uncertain significance (Jul 19, 2023)
3-109304610-C-T		not specified	Uncertain significance (Nov 09, 2023)
3-109304623-T-C		not specified	Likely benign (Feb 19, 2025)
3-109304668-C-T		not specified	Uncertain significance (Dec 24, 2024)
3-109308059-C-T		not specified	Uncertain significance (Nov 07, 2024)
3-109308085-A-C		not specified	Uncertain significance (Mar 19, 2024)
3-109308097-T-C		not specified	Uncertain significance (Aug 02, 2023)
3-109308128-A-T		not specified	Uncertain significance (Apr 06, 2023)
3-109308136-A-G			not provided (-)
3-109308221-C-A			not provided (-)
3-109308256-C-T		not specified	Uncertain significance (Nov 30, 2022)
3-109308265-C-G		not specified	Uncertain significance (Mar 27, 2023)
3-109308281-T-A		not specified	Uncertain significance (Nov 10, 2022)
3-109309030-C-T			Benign (Mar 29, 2018)
3-109309073-C-T		not specified	Uncertain significance (Aug 14, 2024)
3-109309192-A-T		not specified	Uncertain significance (Jan 21, 2025)
3-109309225-C-G		not specified	Likely benign (Oct 01, 2024)
3-109309226-A-G		not specified	Uncertain significance (Dec 14, 2024)
3-109309277-T-C		not specified	Uncertain significance (Jan 23, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DPPA2	protein_coding	protein_coding	ENST00000478945	7	22730

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.79e-9	0.217	125731	0	15	125746	0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.164	162	168	0.964	0.00000880	1962
Missense in Polyphen		38	38.688	0.98223		487
Synonymous	0.219	56	58.1	0.964	0.00000321	555
Loss of Function	0.495	14	16.1	0.867	7.66e-7	199

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000272	0.000272
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000358	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.0000980	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds to target gene promoters, including NKX2-5 and SYCE1, but not GATA4, and may be involved in the maintenance of the active epigenetic status of these genes. {ECO:0000250}.

Recessive Scores

• pRec: 0.0880

Intolerance Scores

• loftool: 0.762
• rvis_EVS: 0.31
• rvis_percentile_EVS: 72.23

Haploinsufficiency Scores

• pHI: 0.0684
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.963

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dppa2
• 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); normal phenotype; respiratory system phenotype; growth/size/body region phenotype; homeostasis/metabolism phenotype; cellular phenotype

Gene ontology

• Cellular component: nucleus
• Molecular function: chromatin binding