LRRC47

Chr 1

leucine rich repeat containing 47

NCBI Gene: 57470 ENSG00000130764 UniProt: Q8N1G4 OMIM: 619154

The protein enables RNA binding and is predicted to be involved in phenylalanyl-tRNA aminoacylation, a process essential for protein synthesis. Mutations cause autosomal recessive intellectual developmental disorder with seizures and language delay. This gene is highly constrained against loss-of-function variants (pLI 0.87, LOEUF 0.41), indicating that complete loss of function is likely not tolerated.

OMIM ResearchSummary from RefSeq

Enables RNA binding activity. Predicted to be involved in phenylalanyl-tRNA aminoacylation. [provided by Alliance of Genome Resources, Jul 2025]

OMIM ResearchGenerating clinical summary…

LOEUF 0.41

Clinical Summary— LRRC47

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Population Constraint (gnomAD)

Moderately constrained gene (pLI 0.87) — some intolerance to loss-of-function variants.

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ClinVar Variants

77 VUS of 93 total submissions

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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Moderate LoF intolerance

LoF Constraint?

0.41LOEUF

pLI 0.871

Z-score 3.17

OE 0.13 (0.05–0.41)

Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint?

1.03Z-score

OE missense 0.84 (0.76–0.93)

263 obs / 314.2 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.13 (0.05–0.41)

0≤0.351.4

Missense OE?0.84 (0.76–0.93)

0≤0.61.4

Synonymous OE?1.08

0≤1.21.6

LoF obs/exp: 2 / 15.5Missense obs/exp: 263 / 314.2Syn Z: -0.71

ClinVar Variant Classifications

93 submitted variants in ClinVar

ClinVar

Classification Summary

VUS77

Likely Benign1

VUS

Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	Missense + Inframe	Total
Pathogenic	0	0
Likely Pathogenic	0	0
VUS	77	77
Likely Benign	1	1
Benign	0	0
Total	78	78

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

View in ClinVar →

90 pathogenic / likely-pathogenic (of 104) ClinVar copy-number / structural variants overlap LRRC47 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →