EP400P1

EP400 pseudogene 1

Basic information

Region (hg38): 12:132104021-132127177

Previous symbols: [ "EP400NL" ]

Links

ENSG00000185684 ∙ NCBI:347918 ∙ ∙ HGNC:26602 ∙ Uniprot:Q6ZTU2 ∙ 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 EP400P1 gene.

• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EP400P1 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						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	0	1	0

Variants in EP400P1

This is a list of pathogenic ClinVar variants found in the EP400P1 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-132105065-G-T			Likely benign (Mar 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EP400P1	protein_coding	protein_coding	ENST00000443539	3	44202

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000447	0.409	124933	5	751	125689	0.00301

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.869	155	189	0.822	0.0000111	2283
Missense in Polyphen		45	67.156	0.67008		908
Synonymous	0.228	88	90.8	0.970	0.00000633	749
Loss of Function	0.478	9	10.7	0.842	5.28e-7	122

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00540	0.00528
Ashkenazi Jewish	0.000997	0.000993
East Asian	0.00	0.00
Finnish	0.000927	0.000924
European (Non-Finnish)	0.00464	0.00458
Middle Eastern	0.00	0.00
South Asian	0.000788	0.000784
Other	0.00443	0.00441

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• pHI: 0.116
• hipred: N
• hipred_score: 0.187

Essentials

• essential_gene_gene_trap: N