GPRIN1
Basic information
Region (hg38): 5:176595802-176610156
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the GPRIN1 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 | |||||
missense | 92 | 98 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 2 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 92 | 7 | 2 |
Variants in GPRIN1
This is a list of pathogenic ClinVar variants found in the GPRIN1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
5-176596840-A-C | not specified | Uncertain significance (Sep 11, 2024) | ||
5-176596854-A-G | not specified | Uncertain significance (Jan 22, 2024) | ||
5-176596856-A-C | not specified | Uncertain significance (Dec 27, 2023) | ||
5-176596858-T-A | not specified | Uncertain significance (Jan 22, 2024) | ||
5-176596915-C-T | not specified | Uncertain significance (Jul 31, 2023) | ||
5-176596939-C-T | not specified | Uncertain significance (Aug 04, 2024) | ||
5-176596983-C-G | not specified | Uncertain significance (Jul 30, 2024) | ||
5-176596984-G-A | not specified | Uncertain significance (Jan 20, 2025) | ||
5-176597118-G-A | not specified | Uncertain significance (Jul 14, 2021) | ||
5-176597125-G-T | not specified | Uncertain significance (Feb 15, 2023) | ||
5-176597136-G-A | not specified | Uncertain significance (Oct 03, 2022) | ||
5-176597148-G-T | not specified | Uncertain significance (May 24, 2024) | ||
5-176597164-C-T | not specified | Uncertain significance (May 02, 2024) | ||
5-176597173-C-T | not specified | Uncertain significance (Jul 05, 2024) | ||
5-176597190-G-A | not specified | Uncertain significance (Jan 26, 2025) | ||
5-176597196-G-A | not specified | Uncertain significance (Jan 07, 2022) | ||
5-176597203-G-T | not specified | Uncertain significance (Aug 06, 2024) | ||
5-176597209-T-C | not specified | Uncertain significance (Oct 03, 2022) | ||
5-176597232-G-T | not specified | Uncertain significance (May 04, 2022) | ||
5-176597240-G-A | Likely benign (May 01, 2022) | |||
5-176597244-C-T | not specified | Uncertain significance (Nov 08, 2022) | ||
5-176597263-C-T | not specified | Likely benign (Dec 04, 2024) | ||
5-176597266-C-T | not specified | Uncertain significance (Dec 27, 2022) | ||
5-176597275-G-A | not specified | Uncertain significance (Mar 11, 2025) | ||
5-176597328-C-T | not specified | Uncertain significance (May 23, 2023) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
GPRIN1 | protein_coding | protein_coding | ENST00000303991 | 1 | 14332 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.970 | 0.0300 | 68560 | 8581 | 48607 | 125748 | 0.262 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.338 | 496 | 518 | 0.958 | 0.0000294 | 6278 |
Missense in Polyphen | 85 | 136.12 | 0.62444 | 1968 | ||
Synonymous | 0.307 | 228 | 234 | 0.974 | 0.0000157 | 2313 |
Loss of Function | 3.69 | 2 | 19.7 | 0.102 | 9.88e-7 | 326 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 1.04 | 0.750 |
Ashkenazi Jewish | 0.544 | 0.272 |
East Asian | 0.654 | 0.328 |
Finnish | 0.410 | 0.202 |
European (Non-Finnish) | 0.530 | 0.266 |
Middle Eastern | 0.654 | 0.328 |
South Asian | 0.541 | 0.269 |
Other | 0.544 | 0.268 |
dbNSFP
Source:
- Function
- FUNCTION: May be involved in neurite outgrowth. {ECO:0000250}.;
- Pathway
- MECP2 and Associated Rett Syndrome
(Consensus)
Recessive Scores
- pRec
- 0.0800
Intolerance Scores
- loftool
- 0.487
- rvis_EVS
- 0.16
- rvis_percentile_EVS
- 64.92
Haploinsufficiency Scores
- pHI
- 0.0971
- hipred
- Y
- hipred_score
- 0.519
- ghis
- 0.553
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.0646
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Gprin1
- Phenotype
Gene ontology
- Biological process
- neuron projection development
- Cellular component
- plasma membrane;growth cone
- Molecular function
- phosphoprotein binding