LRRC59

leucine rich repeat containing 59

Basic information

Region (hg38): 17:50375059-50397523

Links

ENSG00000108829 ∙ NCBI:55379 ∙ OMIM:614854 ∙ HGNC:28817 ∙ Uniprot:Q96AG4 ∙ 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 LRRC59 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRRC59 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			22	1		23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	1	0

Variants in LRRC59

This is a list of pathogenic ClinVar variants found in the LRRC59 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-50375223-G-T			Benign (Oct 10, 2018)
17-50375279-C-G		not specified	Uncertain significance (May 04, 2023)
17-50375327-G-A		not specified	Uncertain significance (Jun 14, 2022)
17-50375332-G-A		not specified	Uncertain significance (Sep 27, 2021)
17-50375405-C-T		not specified	Uncertain significance (Jul 07, 2022)
17-50375410-C-G		not specified	Uncertain significance (Dec 16, 2023)
17-50375476-G-A		not specified	Uncertain significance (Apr 05, 2023)
17-50375525-C-A		not specified	Uncertain significance (Feb 10, 2022)
17-50375532-G-C		not specified	Uncertain significance (Mar 20, 2024)
17-50375539-A-C		not specified	Uncertain significance (Oct 06, 2021)
17-50375588-A-G		not specified	Uncertain significance (Aug 09, 2021)
17-50375659-C-T		not specified	Likely benign (Mar 20, 2023)
17-50375665-A-G		not specified	Uncertain significance (Feb 27, 2024)
17-50375732-C-T		not specified	Uncertain significance (Oct 26, 2021)
17-50375810-C-T		not specified	Uncertain significance (Apr 08, 2024)
17-50375912-C-T		not specified	Uncertain significance (Oct 10, 2023)
17-50375962-A-G		not specified	Likely benign (Jun 21, 2023)
17-50375974-C-G		not specified	Uncertain significance (Oct 29, 2021)
17-50376135-T-C		not specified	Uncertain significance (Feb 16, 2023)
17-50376141-C-T		not specified	Likely benign (Nov 12, 2021)
17-50376153-C-T		not specified	Uncertain significance (Jan 23, 2024)
17-50376186-C-T		not specified	Likely benign (Jul 14, 2023)
17-50378625-G-A		not specified	Uncertain significance (Mar 17, 2023)
17-50378783-G-A		not specified	Uncertain significance (Feb 28, 2024)
17-50379083-C-G		not specified	Uncertain significance (Jan 04, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRRC59	protein_coding	protein_coding	ENST00000225972	7	22495

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.434	0.564	125743	0	5	125748	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.15	147	192	0.766	0.0000123	1974
Missense in Polyphen		26	53.087	0.48976		635
Synonymous	1.98	53	74.8	0.708	0.00000380	630
Loss of Function	2.74	3	14.1	0.213	6.78e-7	173

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.000109	0.000109
South Asian	0.0000654	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for nuclear import of FGF1, but not that of FGF2. Might regulate nuclear import of exogenous FGF1 by facilitating interaction with the nuclear import machinery and by transporting cytosolic FGF1 to, and possibly through, the nuclear pores. {ECO:0000269|PubMed:22321063}.
• Pathway: Fibroblast growth factor-1 (Consensus)

Recessive Scores

• pRec: 0.126

Intolerance Scores

• loftool: 0.405
• rvis_EVS: -0.34
• rvis_percentile_EVS: 30.07

Haploinsufficiency Scores

• pHI: 0.0979
• hipred: Y
• hipred_score: 0.728
• ghis: 0.603

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.966

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lrrc59

Gene ontology

• Cellular component: nuclear envelope;cytoplasm;endoplasmic reticulum;endoplasmic reticulum membrane;membrane;integral component of membrane;organelle membrane;mitochondrial nucleoid
• Molecular function: RNA binding;cadherin binding