LRRD1

leucine rich repeats and death domain containing 1

Basic information

Region (hg38): 7:92141643-92179531

Links

ENSG00000240720 ∙ NCBI:401387 ∙ ∙ HGNC:34300 ∙ Uniprot:A4D1F6 ∙ 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 LRRD1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRRD1 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			34	2		36
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	35	2	0

Variants in LRRD1

This is a list of pathogenic ClinVar variants found in the LRRD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-92144927-T-C		not specified	Uncertain significance (May 02, 2023)
7-92150573-T-C		not specified	Uncertain significance (Dec 14, 2021)
7-92150575-T-C		not specified	Uncertain significance (Aug 28, 2023)
7-92150639-T-C		not specified	Uncertain significance (Sep 27, 2021)
7-92159112-A-G		not specified	Uncertain significance (Apr 04, 2024)
7-92159142-T-C		not specified	Uncertain significance (Nov 17, 2023)
7-92159178-G-C		not specified	Uncertain significance (May 26, 2022)
7-92163350-G-A		not specified	Uncertain significance (Aug 30, 2021)
7-92163370-G-T		not specified	Uncertain significance (Oct 25, 2022)
7-92163371-C-A		not specified	Uncertain significance (Sep 27, 2021)
7-92163443-G-A		not specified	Uncertain significance (Apr 06, 2023)
7-92163471-A-C		not specified	Uncertain significance (Dec 13, 2022)
7-92163489-G-A		not specified	Uncertain significance (Mar 24, 2023)
7-92163527-T-C		not specified	Uncertain significance (Jun 03, 2024)
7-92163531-G-A		not specified	Uncertain significance (Jul 14, 2023)
7-92163570-T-A		not specified	Uncertain significance (Jul 09, 2021)
7-92163571-T-G		not specified	Uncertain significance (Jul 09, 2021)
7-92163740-G-C		not specified	Uncertain significance (Dec 01, 2022)
7-92163781-G-T		not specified	Uncertain significance (Mar 22, 2023)
7-92163800-T-G		not specified	Uncertain significance (Dec 07, 2021)
7-92163854-C-G		not specified	Uncertain significance (Jan 10, 2023)
7-92163896-C-T		not specified	Uncertain significance (Dec 03, 2021)
7-92164004-A-G		not specified	Uncertain significance (Mar 02, 2023)
7-92164131-C-T		not specified	Uncertain significance (Dec 07, 2021)
7-92164150-T-C		not specified	Likely benign (Jul 09, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRRD1	protein_coding	protein_coding	ENST00000458448	5	67373

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000168	0.967	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.53	253	331	0.763	0.0000150	5642
Missense in Polyphen		55	71.794	0.76608		1361
Synonymous	1.50	101	122	0.827	0.00000556	1591
Loss of Function	1.99	13	23.4	0.555	0.00000104	464

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

• rvis_EVS: 0.26
• rvis_percentile_EVS: 69.83

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lrrd1

Gene ontology

• Biological process: signal transduction
• Cellular component: cytoplasm