EIPR1

EARP complex and GARP complex interacting protein 1, the group of WD repeat domain containing

Basic information

Region (hg38): 2:3188925-3377830

Previous symbols: [ "TSSC1" ]

Links

ENSG00000032389 ∙ NCBI:7260 ∙ OMIM:608998 ∙ HGNC:12383 ∙ Uniprot:Q53HC9 ∙ 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 EIPR1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EIPR1 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				1		1
missense			14			14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	1	0

Variants in EIPR1

This is a list of pathogenic ClinVar variants found in the EIPR1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-3189450-C-T		not specified	Uncertain significance (Sep 17, 2021)
2-3192472-C-T		not specified	Uncertain significance (Jun 06, 2022)
2-3192568-G-A		not specified	Uncertain significance (Dec 12, 2023)
2-3194079-G-A			Likely benign (Jul 01, 2022)
2-3194090-A-C		not specified	Uncertain significance (Dec 22, 2023)
2-3196968-G-A		not specified	Uncertain significance (Sep 25, 2023)
2-3197004-G-A		not specified	Uncertain significance (Jun 10, 2022)
2-3257324-T-C		not specified	Uncertain significance (May 27, 2022)
2-3257381-A-G		not specified	Uncertain significance (May 23, 2024)
2-3257423-C-A		not specified	Uncertain significance (Dec 21, 2021)
2-3257423-C-T		not specified	Uncertain significance (Dec 19, 2023)
2-3338044-C-T		not specified	Uncertain significance (Dec 27, 2023)
2-3338088-T-C		not specified	Uncertain significance (Dec 16, 2023)
2-3354591-G-A		not specified	Uncertain significance (Nov 09, 2022)
2-3354609-C-A		not specified	Uncertain significance (Dec 27, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EIPR1	protein_coding	protein_coding	ENST00000382125	9	188958

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0636	0.936	125736	0	12	125748	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.55	168	235	0.715	0.0000140	2567
Missense in Polyphen		78	128.44	0.6073		1370
Synonymous	1.17	87	102	0.852	0.00000715	719
Loss of Function	3.01	6	20.8	0.288	9.75e-7	227

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000106	0.000105
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a component of endosomal retrieval machinery that is involved in protein transport from early endosomes to either recycling endosomes or the trans-Golgi network. Mediates the recruitment of Golgi-associated retrograde protein (GARP) complex to the trans-Golgi network and controls early endosome-to- Golgi transport of internalized protein. Promotes the recycling of internalized transferrin receptor (TFRC) to the plasma membrane through interaction with endosome-associated recycling protein (EARP) complex. {ECO:0000269|PubMed:27440922}.

Recessive Scores

• pRec: 0.112

Intolerance Scores

• rvis_EVS: -0.96
• rvis_percentile_EVS: 9.09

Haploinsufficiency Scores

• pHI: 0.181
• hipred: Y
• hipred_score: 0.625
• ghis: 0.643

Essentials

• essential_gene_gene_trap: K

Mouse Genome Informatics

• Gene name: Eipr1

Gene ontology

• Biological process: protein ubiquitination
• Cellular component: Golgi apparatus