LRRC49

leucine rich repeat containing 49, the group of Tubulin polyglutamylase complex subunits

Basic information

Region (hg38): 15:70853238-71053658

Links

ENSG00000137821 ∙ NCBI:54839 ∙ ∙ HGNC:25965 ∙ Uniprot:Q8IUZ0 ∙ 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 LRRC49 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRRC49 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			32			32
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	32	0	0

Variants in LRRC49

This is a list of pathogenic ClinVar variants found in the LRRC49 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-70853890-T-C		not specified	Uncertain significance (Aug 16, 2022)
15-70853896-C-G		not specified	Uncertain significance (Nov 21, 2022)
15-70853949-G-A		not specified	Uncertain significance (Aug 26, 2022)
15-70853965-C-G		not specified	Uncertain significance (Aug 13, 2021)
15-70853989-C-T		not specified	Uncertain significance (Aug 14, 2023)
15-70854076-C-G		not specified	Uncertain significance (Jun 02, 2023)
15-70882482-G-A		not specified	Uncertain significance (Feb 15, 2023)
15-70882564-G-C		not specified	Uncertain significance (Jan 17, 2023)
15-70882594-T-C		not specified	Uncertain significance (Dec 07, 2021)
15-70882769-C-T		not specified	Uncertain significance (May 02, 2024)
15-70882827-A-C		not specified	Uncertain significance (Jan 09, 2024)
15-70882904-G-A		not specified	Uncertain significance (Sep 16, 2021)
15-70891870-C-A		not specified	Uncertain significance (Jun 11, 2021)
15-70891879-G-A		not specified	Uncertain significance (Jun 28, 2023)
15-70891911-G-C		not specified	Uncertain significance (Jan 08, 2024)
15-70891959-T-A		not specified	Uncertain significance (Feb 16, 2023)
15-70891987-C-A		not specified	Uncertain significance (Nov 13, 2023)
15-70892001-C-T		not specified	Uncertain significance (Aug 17, 2022)
15-70892071-C-T		not specified	Uncertain significance (Mar 11, 2022)
15-70892124-C-A		not specified	Uncertain significance (Apr 04, 2023)
15-70892125-G-A		not specified	Uncertain significance (Dec 21, 2023)
15-70892181-A-G		not specified	Uncertain significance (Jun 16, 2024)
15-70892188-C-T		not specified	Uncertain significance (Dec 01, 2022)
15-70892191-C-T		not specified	Uncertain significance (Mar 23, 2023)
15-70892194-G-A		not specified	Uncertain significance (May 05, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRRC49	protein_coding	protein_coding	ENST00000560369	16	196837

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000935	1.00	125692	0	53	125745	0.000211

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.16	305	367	0.830	0.0000192	4580
Missense in Polyphen		80	114.07	0.70129		1400
Synonymous	-0.0817	132	131	1.01	0.00000670	1267
Loss of Function	3.32	15	36.7	0.408	0.00000182	452

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000210	0.000210
Ashkenazi Jewish	0.00	0.00
East Asian	0.000384	0.000381
Finnish	0.0000467	0.0000462
European (Non-Finnish)	0.000303	0.000299
Middle Eastern	0.000384	0.000381
South Asian	0.000176	0.000163
Other	0.000189	0.000163

dbNSFP

Source: dbNSFP

• Pathway: Post-translational protein modification;Metabolism of proteins;Carboxyterminal post-translational modifications of tubulin (Consensus)

Recessive Scores

• pRec: 0.110

Intolerance Scores

• loftool: 0.790
• rvis_EVS: -0.67
• rvis_percentile_EVS: 15.86

Haploinsufficiency Scores

• pHI: 0.185
• hipred: Y
• hipred_score: 0.601
• ghis: 0.580

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.402

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lrrc49

Gene ontology

• Biological process: outer dynein arm assembly
• Cellular component: cytoplasm;microtubule