GRWD1
Basic information
Region (hg38): 19:48445840-48457022
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- Inborn genetic diseases (21 variants)
- not provided (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.
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 | 21 | 22 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region ? | 0 | |||||
non coding ? | 0 | |||||
Total | 0 | 0 | 21 | 0 | 1 |
Variants in GRWD1
This is a list of pathogenic ClinVar variants found in the GRWD1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
19-48446015-C-T | not specified | Uncertain significance (Sep 23, 2023) | ||
19-48446060-G-A | not specified | Uncertain significance (Sep 22, 2022) | ||
19-48446105-C-T | GRWD1-related disorder | Likely benign (Jun 27, 2019) | ||
19-48446408-A-G | not specified | Uncertain significance (Nov 21, 2022) | ||
19-48446421-A-G | GRWD1-related disorder | Likely benign (Nov 30, 2022) | ||
19-48446429-G-A | not specified | Uncertain significance (Mar 07, 2024) | ||
19-48446727-C-A | not specified | Uncertain significance (Nov 09, 2023) | ||
19-48446764-A-T | not specified | Uncertain significance (Nov 14, 2023) | ||
19-48446772-G-A | not specified | Uncertain significance (Dec 21, 2023) | ||
19-48446778-G-A | not specified | Uncertain significance (Jan 23, 2024) | ||
19-48446829-A-G | not specified | Uncertain significance (Aug 09, 2021) | ||
19-48450389-G-A | not specified | Uncertain significance (Mar 01, 2023) | ||
19-48450424-G-A | not specified | Uncertain significance (Jan 04, 2024) | ||
19-48450437-G-A | Malignant tumor of prostate • not specified | Uncertain significance (Dec 20, 2023) | ||
19-48450512-C-G | not specified | Uncertain significance (Jan 16, 2024) | ||
19-48450515-C-A | not specified | Uncertain significance (Aug 08, 2023) | ||
19-48450520-G-A | not specified | Uncertain significance (Dec 21, 2022) | ||
19-48450669-G-A | not specified | Uncertain significance (Jul 15, 2021) | ||
19-48450680-G-A | not specified | Uncertain significance (Oct 10, 2023) | ||
19-48450686-T-C | not specified | Uncertain significance (Apr 27, 2022) | ||
19-48450722-G-A | not specified | Uncertain significance (Apr 08, 2022) | ||
19-48450724-C-T | GRWD1-related disorder | Likely benign (Jul 31, 2019) | ||
19-48450736-C-T | GRWD1-related disorder | Likely benign (May 24, 2019) | ||
19-48450737-G-A | not specified | Uncertain significance (Mar 16, 2022) | ||
19-48450765-C-T | not specified | Uncertain significance (Sep 06, 2022) |
GnomAD
Source:
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:
- 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
- Phenotype
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