LRRC30

leucine rich repeat containing 30

Basic information

Region (hg38): 18:7231089-7232044

Links

ENSG00000206422 ∙ NCBI:339291 ∙ ∙ HGNC:30219 ∙ Uniprot:A6NM36 ∙ 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 LRRC30 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRRC30 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				1		1
missense			28			28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	28	1	0

Variants in LRRC30

This is a list of pathogenic ClinVar variants found in the LRRC30 region.

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

Position	Type	Phenotype	Significance	ClinVar
18-7231145-G-A		not specified	Uncertain significance (Oct 12, 2021)
18-7231200-C-T		not specified	Uncertain significance (Aug 12, 2021)
18-7231239-T-G		not specified	Uncertain significance (Jun 06, 2023)
18-7231256-C-G		not specified	Uncertain significance (Dec 01, 2022)
18-7231275-G-A		not specified	Uncertain significance (Sep 14, 2022)
18-7231277-G-A		not specified	Uncertain significance (Oct 26, 2022)
18-7231289-G-A		not specified	Uncertain significance (Sep 16, 2021)
18-7231308-C-T		not specified	Uncertain significance (May 23, 2023)
18-7231316-A-G		not specified	Uncertain significance (Mar 13, 2023)
18-7231418-A-G		not specified	Uncertain significance (Jul 08, 2021)
18-7231421-C-T		not specified	Uncertain significance (Apr 12, 2022)
18-7231430-G-A		not specified	Uncertain significance (Nov 20, 2023)
18-7231443-G-C		not specified	Uncertain significance (Nov 10, 2022)
18-7231445-G-C		not specified	Uncertain significance (Aug 02, 2023)
18-7231521-G-T		not specified	Uncertain significance (Jun 23, 2023)
18-7231560-A-G		not specified	Uncertain significance (Jul 14, 2023)
18-7231572-T-C		not specified	Uncertain significance (May 06, 2024)
18-7231664-G-T		not specified	Uncertain significance (Mar 07, 2024)
18-7231671-T-C		not specified	Uncertain significance (May 02, 2024)
18-7231682-G-C		not specified	Uncertain significance (Mar 27, 2023)
18-7231692-T-C		not specified	Uncertain significance (Jun 10, 2024)
18-7231749-G-A		not specified	Uncertain significance (Apr 19, 2023)
18-7231756-G-C		not specified	Uncertain significance (Jul 20, 2021)
18-7231799-A-T		not specified	Uncertain significance (Dec 13, 2022)
18-7231864-T-G		not specified	Uncertain significance (Apr 19, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRRC30	protein_coding	protein_coding	ENST00000383467	1	923

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000190	0.149	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.429	200	184	1.09	0.0000113	1966
Missense in Polyphen		80	61.405	1.3028		741
Synonymous	-0.600	101	93.6	1.08	0.00000652	640
Loss of Function	-0.469	8	6.69	1.20	3.69e-7	72

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.766
• rvis_EVS: 0.17
• rvis_percentile_EVS: 65.96

Haploinsufficiency Scores

• pHI: 0.143
• hipred: N
• hipred_score: 0.251
• ghis: 0.426

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.279

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lrrc30

Gene ontology

• Biological process: protein dephosphorylation
• Cellular component: photoreceptor inner segment;photoreceptor outer segment membrane
• Molecular function: protein serine/threonine phosphatase activity