LRWD1

leucine rich repeats and WD repeat domain containing 1, the group of MicroRNA protein coding host genes|WD repeat domain containing

Basic information

Region (hg38): 7:102464956-102473168

Links

ENSG00000161036 ∙ NCBI:222229 ∙ OMIM:615167 ∙ HGNC:21769 ∙ Uniprot:Q9UFC0 ∙ 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 LRWD1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRWD1 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			45	1	1	47
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	45	2	1

Variants in LRWD1

This is a list of pathogenic ClinVar variants found in the LRWD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-102465103-T-G		not specified	Uncertain significance (Aug 30, 2021)
7-102465127-A-G		not specified	Uncertain significance (Oct 20, 2023)
7-102465129-A-T		not specified	Uncertain significance (Dec 03, 2021)
7-102465866-T-C		not specified	Uncertain significance (May 16, 2024)
7-102465959-C-T		not specified	Uncertain significance (May 02, 2024)
7-102466011-A-G		not specified	Uncertain significance (Feb 27, 2024)
7-102466033-G-C		not specified	Uncertain significance (Dec 27, 2022)
7-102466050-C-T		not specified	Uncertain significance (Jan 04, 2024)
7-102466191-C-T		not specified	Uncertain significance (Oct 04, 2022)
7-102466206-A-G		not specified	Uncertain significance (Dec 06, 2021)
7-102466226-A-G		not specified	Uncertain significance (Jun 29, 2022)
7-102466227-C-T		not specified	Uncertain significance (May 26, 2024)
7-102467367-C-T		not specified	Uncertain significance (Mar 03, 2022)
7-102467382-A-C		not specified	Uncertain significance (Jun 01, 2023)
7-102467403-A-G		not specified	Uncertain significance (Dec 17, 2021)
7-102467444-G-A		not specified	Uncertain significance (Apr 08, 2024)
7-102467750-C-T		not specified	Uncertain significance (Jun 17, 2024)
7-102467758-A-T		not specified	Uncertain significance (Jan 08, 2024)
7-102467788-A-C		not specified	Uncertain significance (Jul 06, 2021)
7-102467789-A-T		not specified	Uncertain significance (May 24, 2024)
7-102468072-C-T		not specified	Likely benign (Apr 23, 2024)
7-102468083-C-T		not specified	Uncertain significance (Jul 05, 2023)
7-102468095-G-A		not specified	Uncertain significance (Jul 09, 2021)
7-102468123-G-A		not specified	Uncertain significance (Dec 17, 2023)
7-102468138-C-T		not specified	Uncertain significance (Dec 16, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRWD1	protein_coding	protein_coding	ENST00000292616	15	8240

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.57e-20	0.00284	125651	0	95	125746	0.000378

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.229	408	395	1.03	0.0000252	4089
Missense in Polyphen		157	161.2	0.97396		1675
Synonymous	-3.30	239	182	1.31	0.0000131	1321
Loss of Function	0.164	31	32.0	0.969	0.00000146	345

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000571	0.000571
Ashkenazi Jewish	0.000498	0.000496
East Asian	0.000281	0.000272
Finnish	0.000424	0.000416
European (Non-Finnish)	0.000510	0.000475
Middle Eastern	0.000281	0.000272
South Asian	0.000289	0.000261
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for G1/S transition. Recruits and stabilizes the origin recognition complex (ORC) onto chromatin during G1 to establish pre-replication complex (preRC) and to heterochromatic sites in post-replicated cells. Binds a combination of DNA and histone methylation repressive marks on heterochromatin. Binds histone H3 and H4 trimethylation marks H3K9me3, H3K27me3 and H4K20me3 in a cooperative manner with DNA methylation. Required for silencing of major satellite repeats. May be important ORC2, ORC3 and ORC4 stability. {ECO:0000269|PubMed:20850016, ECO:0000269|PubMed:20932478, ECO:0000269|PubMed:21029866, ECO:0000269|PubMed:22427655, ECO:0000269|PubMed:22645314}.

Intolerance Scores

• loftool: 0.815
• rvis_EVS: 0.03
• rvis_percentile_EVS: 55.83

Haploinsufficiency Scores

• pHI: 0.134
• hipred: N
• hipred_score: 0.282
• ghis: 0.432

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.492

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lrwd1

Gene ontology

• Biological process: DNA replication initiation;chromatin organization;establishment of protein localization to chromatin
• Cellular component: kinetochore;condensed chromosome kinetochore;nucleus;nuclear origin of replication recognition complex;pericentric heterochromatin;nucleolus;cytoplasm;microtubule organizing center;telomeric heterochromatin;intracellular membrane-bounded organelle
• Molecular function: chromatin binding;protein binding;methyl-CpG binding;methylated histone binding