ECRG4

ECRG4 augurin precursor

Basic information

Region (hg38): 2:106063246-106078155

Previous symbols: [ "C2orf40" ]

Links

ENSG00000119147 ∙ NCBI:84417 ∙ OMIM:611752 ∙ HGNC:24642 ∙ Uniprot:Q9H1Z8 ∙ 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 ECRG4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ECRG4 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			2		1	3
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	2	0	1

Variants in ECRG4

This is a list of pathogenic ClinVar variants found in the ECRG4 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-106073898-C-G		not specified	Uncertain significance (Aug 09, 2021)
2-106073912-G-A			Benign (Oct 19, 2017)
2-106077850-A-T		not specified	Uncertain significance (Aug 10, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ECRG4	protein_coding	protein_coding	ENST00000238044	4	14914

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000405	0.654	123522	65	2161	125748	0.00889

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.164	88	83.8	1.05	0.00000533	945
Missense in Polyphen		32	31.737	1.0083		354
Synonymous	-1.29	41	31.7	1.29	0.00000193	276
Loss of Function	0.728	6	8.26	0.727	4.49e-7	87

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000416	0.000416
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0710	0.0708
European (Non-Finnish)	0.00282	0.00283
Middle Eastern	0.0000544	0.0000544
South Asian	0.0123	0.0122
Other	0.00733	0.00736

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable hormone that may induce senescence of oligodendrocyte and neural precursor cells, characterized by G1 arrest, RB1 dephosphorylation and accelerated CCND1 and CCND3 proteasomal degradation. {ECO:0000250, ECO:0000269|PubMed:17284679}.

Recessive Scores

• pRec: 0.113

Intolerance Scores

• loftool: 0.792
• rvis_EVS: 0.77
• rvis_percentile_EVS: 86.95

Haploinsufficiency Scores

• pHI: 0.161
• hipred: N
• hipred_score: 0.378
• ghis: 0.407

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: 1500015O10Rik
• Phenotype: normal phenotype

Zebrafish Information Network

• Gene name: ecrg4a
• Affected structure: fourth ventricle
• Phenotype tag: abnormal
• Phenotype quality: hydrocephalic

Gene ontology

• Biological process: anaphase-promoting complex-dependent catabolic process;G1 to G0 transition;cellular senescence
• Cellular component: extracellular space;transport vesicle