LRRC27

leucine rich repeat containing 27

Basic information

Region (hg38): 10:132332154-132381508

Links

ENSG00000148814 ∙ NCBI:80313 ∙ ∙ HGNC:29346 ∙ Uniprot:Q9C0I9 ∙ 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 LRRC27 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRRC27 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				2		2
missense			37	6		43
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	37	8	0

Variants in LRRC27

This is a list of pathogenic ClinVar variants found in the LRRC27 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-132333549-G-A		not specified	Uncertain significance (Mar 25, 2024)
10-132333586-C-A		not specified	Uncertain significance (Dec 12, 2023)
10-132333622-A-G		not specified	Likely benign (Jan 23, 2024)
10-132333673-T-C		not specified	Uncertain significance (Jun 07, 2024)
10-132333684-G-C		not specified	Likely benign (Jul 20, 2021)
10-132333730-T-G		not specified	Uncertain significance (Nov 29, 2023)
10-132337584-A-G		not specified	Uncertain significance (Jul 14, 2021)
10-132337638-G-C		not specified	Uncertain significance (Nov 07, 2022)
10-132337649-C-T		not specified	Uncertain significance (Oct 29, 2021)
10-132337650-G-A		not specified	Uncertain significance (Jun 19, 2024)
10-132337655-A-G		not specified	Uncertain significance (Aug 05, 2023)
10-132342227-T-C		not specified	Uncertain significance (May 26, 2024)
10-132344509-A-G		not specified	Uncertain significance (Nov 21, 2023)
10-132344534-A-G		not specified	Uncertain significance (Aug 16, 2021)
10-132344593-C-T		not specified	Uncertain significance (Dec 20, 2023)
10-132344639-C-G		not specified	Uncertain significance (Dec 20, 2023)
10-132348032-G-A		not specified	Uncertain significance (Jan 26, 2022)
10-132348050-A-G		not specified	Uncertain significance (Jan 26, 2022)
10-132348079-G-A		not specified	Uncertain significance (Jan 06, 2023)
10-132348087-C-A		not specified	Uncertain significance (Aug 22, 2023)
10-132348127-C-T		not specified	Uncertain significance (Mar 29, 2022)
10-132348137-A-G		not specified	Uncertain significance (Feb 17, 2024)
10-132348154-G-C		not specified	Uncertain significance (Sep 21, 2023)
10-132348247-G-A		not specified	Uncertain significance (Sep 22, 2021)
10-132348259-G-A		not specified	Uncertain significance (Feb 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRRC27	protein_coding	protein_coding	ENST00000368614	10	49397

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.01e-17	0.00481	125291	4	453	125748	0.00182

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.589	334	305	1.09	0.0000179	3431
Missense in Polyphen		101	92.888	1.0873		1128
Synonymous	-1.11	141	125	1.13	0.00000805	1051
Loss of Function	-0.0332	26	25.8	1.01	0.00000153	288

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00141	0.00135
Ashkenazi Jewish	0.000405	0.000397
East Asian	0.000817	0.000816
Finnish	0.00	0.00
European (Non-Finnish)	0.000469	0.000466
Middle Eastern	0.000817	0.000816
South Asian	0.0116	0.0115
Other	0.000490	0.000489

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.985
• rvis_EVS: -0.79
• rvis_percentile_EVS: 12.57

Haploinsufficiency Scores

• pHI: 0.0651
• hipred: N
• hipred_score: 0.123
• ghis: 0.501

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0138

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lrrc27