EIPR1

protein-coding

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

Gene summary

This gene has been reported in PMID 9403053 as one of several tumor-suppressing subtransferable fragments located in the imprinted gene domain of 11p15.5, an important tumor-suppressor gene region. Alterations in this region have been associated with the Beckwith-Wiedemann syndrome, Wilms tumor, rhabdomyosarcoma, adrenocortical carcinoma, and lung, ovarian, and breast cancer. Alignment of this gene to genomic sequence data suggests that this gene resides on chromosome 2 rather than chromosome 11. [provided by RefSeq, Dec 2008]

Previous symbols:

TSSC1

MANE transcript

NM_003310.5

Inheritance

—

ClinVar variants

P:4U:56B:2

Top phenotype

NEURODEVELOPMENTAL DISORDER WITH SPASTICITY, HYPOPLASIA OF THE CORPUS CALLOSUM, AND RECURRENT INFECTIONS

gnomAD constraint

pLI —, LoF o/e 0.29

Max pathogenic AF

—

Genomic locus

chr2:3,188,925-3,377,830

External References & Databases

Ensembl (ENSG00000032389)

Transcript & Mutation Effects

hg38 • Region Span ~188.9 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to EIPR1 variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 51

NEURODEVELOPMENTAL DISORDER WITH SPASTICITY, HYPOPLASIA OF THE CORPUS CALLOSUM, AND RECURRENT INFECTIONSTotal: 5

not providedTotal: 1

Neurodevelopmental delay with neutropeniaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_003310.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	1 clinvar		3
missense	4 clinvar		53 clinvar	1 clinvar		58
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	4	0	56	2	0	62

Highest pathogenic variant AF is 0.000019157376

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 31 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_003310.5	RefSeq	NP_003301.1	9	MANE Select
ENST00000382125.9	Ensembl	ENSP00000371559.4	9	MANE Select
NM_001330530.3	RefSeq	NP_001317459.1	10	Standard
NM_001330531.3	RefSeq	NP_001317460.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

protein ubiquitination

Cellular Component

Golgi apparatus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000382125
Coding exons: 9
Length: 188958
Individuals with no LoFs: 125736
Homozygous LoFs: 0
Heterozygous LoFs: 12
Defined: 125748
p: 0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.55	168	235	0.715	0.0000140	2567
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.00011	0.00011	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (gene trap): K