GRWD1

glutamate rich WD repeat containing 1, the group of WD repeat domain containing

Basic information

Region (hg38): 19:48445841-48457022

Links

ENSG00000105447 ∙ NCBI:83743 ∙ OMIM:610597 ∙ HGNC:21270 ∙ Uniprot:Q9BQ67 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• congenital diarrhea (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the GRWD1 gene.

• not_specified (82 variants)
• GRWD1-related_disorder (10 variants)
• Congenital_diarrhea (2 variants)
• Diarrhea_14,_congenital (2 variants)
• not_provided (1 variants)
• Prostate_cancer (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GRWD1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000031485.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				8		8
missense		2	80	1	1	84
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	2	80	9	1

Highest pathogenic variant AF is 0.000245347

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GRWD1	protein_coding	protein_coding	ENST00000253237	7	11250

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000397	0.991	125628	0	120	125748	0.000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.104	282	287	0.983	0.0000180	2853
Missense in Polyphen		86	96.583	0.89043		1009
Synonymous	0.0874	124	125	0.990	0.00000830	920
Loss of Function	2.33	9	20.3	0.443	9.63e-7	206

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000476	0.000476
Ashkenazi Jewish	0.00258	0.00258
East Asian	0.00109	0.00109
Finnish	0.00	0.00
European (Non-Finnish)	0.000515	0.000510
Middle Eastern	0.00109	0.00109
South Asian	0.0000327	0.0000327
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Histone binding-protein that regulates chromatin dynamics and minichromosome maintenance (MCM) loading at replication origins, possibly by promoting chromatin openness (PubMed:25990725). {ECO:0000269|PubMed:25990725}.

Recessive Scores

• pRec: 0.124

Intolerance Scores

• loftool: 0.692
• rvis_EVS: -0.38
• rvis_percentile_EVS: 28.01

Haploinsufficiency Scores

• pHI: 0.240
• hipred: Y
• hipred_score: 0.771
• ghis: 0.565

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.962

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Grwd1

Gene ontology

• Biological process: DNA replication;nucleosome assembly;nucleosome disassembly
• Cellular component: nucleus;chromosome;nucleolus;cytosol;protein-containing complex
• Molecular function: chromatin binding;DNA replication origin binding;RNA binding;protein binding;histone binding