DPPA5

developmental pluripotency associated 5

Basic information

Region (hg38): 6:73353063-73354276

Links

ENSG00000203909 ∙ NCBI:340168 ∙ OMIM:611111 ∙ HGNC:19201 ∙ Uniprot:A6NC42 ∙ 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 DPPA5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DPPA5 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			7			7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	0	0

Variants in DPPA5

This is a list of pathogenic ClinVar variants found in the DPPA5 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-73353345-A-G		not specified	Uncertain significance (Jan 21, 2025)
6-73353369-T-C		not specified	Uncertain significance (Sep 27, 2021)
6-73353370-T-G		not specified	Uncertain significance (Oct 04, 2022)
6-73353864-C-T		not specified	Uncertain significance (Jan 02, 2025)
6-73353870-C-T		not specified	Uncertain significance (Sep 01, 2024)
6-73353913-G-C		not specified	Uncertain significance (Jun 12, 2023)
6-73353931-C-T		Aganglionic megacolon	Uncertain significance (May 16, 2019)
6-73354018-G-C		not specified	Uncertain significance (Sep 30, 2024)
6-73354029-G-A		not specified	Uncertain significance (Jan 03, 2022)
6-73354143-A-C		not specified	Uncertain significance (Nov 14, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DPPA5	protein_coding	protein_coding	ENST00000370370	3	1234

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00406	0.669	125732	0	13	125745	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.22	50	81.0	0.617	0.00000568	742
Missense in Polyphen		6	10.204	0.58801		138
Synonymous	0.748	29	34.6	0.838	0.00000265	228
Loss of Function	0.606	4	5.54	0.722	3.01e-7	57

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000616	0.0000615
Middle Eastern	0.000109	0.000109
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in the maintenance of embryonic stem (ES) cell pluripotency. Dispensable for self-renewal of pluripotent ES cells and establishment of germ cells. Associates with specific target mRNAs (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.104

Intolerance Scores

• loftool: 0.716
• rvis_EVS: 0.26
• rvis_percentile_EVS: 69.83

Haploinsufficiency Scores

• pHI: 0.123
• hipred: N
• hipred_score: 0.238

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.185

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dppa5a
• Phenotype: normal phenotype

Gene ontology

• Biological process: multicellular organism development
• Cellular component: cytoplasm
• Molecular function: RNA binding