LRRC28

leucine rich repeat containing 28

Basic information

Region (hg38): 15:99251362-99390729

Links

ENSG00000168904 ∙ NCBI:123355 ∙ ∙ HGNC:28355 ∙ Uniprot:Q86X40 ∙ 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 LRRC28 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRRC28 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			17			17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	0	0

Variants in LRRC28

This is a list of pathogenic ClinVar variants found in the LRRC28 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-99255967-G-A		not specified	Uncertain significance (Dec 16, 2023)
15-99256017-G-C		not specified	Uncertain significance (Jan 09, 2024)
15-99256032-G-T		not specified	Uncertain significance (Jan 07, 2022)
15-99256073-G-T		not specified	Uncertain significance (Apr 19, 2024)
15-99287262-T-G		not specified	Uncertain significance (May 21, 2024)
15-99287273-A-G		not specified	Uncertain significance (Jun 10, 2024)
15-99287280-T-C		not specified	Uncertain significance (Jan 02, 2024)
15-99287834-C-T		not specified	Uncertain significance (Dec 18, 2023)
15-99287839-A-T		not specified	Uncertain significance (Sep 14, 2022)
15-99333926-T-A		not specified	Uncertain significance (May 17, 2023)
15-99333970-C-T		not specified	Uncertain significance (Jan 05, 2022)
15-99361400-G-A		not specified	Uncertain significance (Dec 17, 2023)
15-99361427-A-G		not specified	Uncertain significance (Dec 08, 2023)
15-99361448-G-A		not specified	Uncertain significance (Jul 21, 2021)
15-99361472-A-G		not specified	Uncertain significance (Aug 02, 2022)
15-99363159-C-T		not specified	Uncertain significance (Apr 27, 2022)
15-99363237-G-A		not specified	Uncertain significance (Jun 29, 2023)
15-99363246-A-G		not specified	Uncertain significance (Jun 02, 2023)
15-99386037-A-G		not specified	Uncertain significance (Mar 23, 2023)
15-99386040-G-C		not specified	Uncertain significance (Jul 20, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRRC28	protein_coding	protein_coding	ENST00000301981	9	139368

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.01e-11	0.124	125708	1	39	125748	0.000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0257	203	202	1.01	0.0000113	2358
Missense in Polyphen		47	58.648	0.8014		720
Synonymous	-0.785	95	85.7	1.11	0.00000495	750
Loss of Function	0.538	18	20.6	0.872	0.00000124	232

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000330	0.000329
Ashkenazi Jewish	0.00	0.00
East Asian	0.000164	0.000163
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000141	0.000141
Middle Eastern	0.000164	0.000163
South Asian	0.000360	0.000327
Other	0.000331	0.000326

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.118

Intolerance Scores

• loftool: 0.704
• rvis_EVS: -0.4
• rvis_percentile_EVS: 26.53

Haploinsufficiency Scores

• pHI: 0.128
• hipred: N
• hipred_score: 0.394
• ghis: 0.567

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.598

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lrrc28