EIPR1

Chr 2AR

EARP complex and GARP complex interacting protein 1

Also known as: EIPR-1, NEDSCI, TSSC1

NCBI Gene: 7260 ENSG00000032389 UniProt: Q53HC9 OMIM: 608998

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]

OMIM Research

OMIM ResearchGenerating clinical summary…

DNmechanismARLOEUF 0.571 OMIM phenotype

Clinical Summary— EIPR1

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Population Constraint (gnomAD)

Constrained for loss-of-function variants (OE-LoF 0.29) despite low pLI — interpret in context.

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ClinVar Variants

4 unique Pathogenic / Likely Pathogenic· 51 VUS of 69 total submissions

Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Moderate LoF intolerance

LoF Constraint?

0.57LOEUF

pLI 0.064

Z-score 3.01

OE 0.29 (0.16–0.57)

Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint?

1.55Z-score

OE missense 0.72 (0.63–0.81)

168 obs / 235.0 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.29 (0.16–0.57)

0≤0.351.4

Missense OE?0.72 (0.63–0.81)

0≤0.61.4

Synonymous OE?0.85

0≤1.21.6

LoF obs/exp: 6 / 20.8Missense obs/exp: 168 / 235.0Syn Z: 1.17

This gene — mechanism propensity

0.6454th %ile

GOF

0.4578th %ile

LOF

0.4038th %ile

The highest-scoring mechanism for this gene is dominant-negative.

DNprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

69 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic4

VUS51

Likely Benign2

Pathogenic

VUS

Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	Missense + Inframe	Synonymous	Total
Pathogenic	4	0	4
Likely Pathogenic	0	0	0
VUS	51	0	51
Likely Benign	1	1	2
Benign	0	0	0
Total	56	1	57

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

27 pathogenic / likely-pathogenic (of 45) ClinVar copy-number / structural variants overlap EIPR1 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →