PSRC1
Basic information
Region (hg38): 1:109279556-109283186
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 PSRC1 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 | 27 | 29 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 27 | 2 | 0 |
Variants in PSRC1
This is a list of pathogenic ClinVar variants found in the PSRC1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
1-109280405-C-T | not specified | Uncertain significance (Oct 26, 2022) | ||
1-109280450-G-A | not specified | Uncertain significance (Apr 18, 2023) | ||
1-109280783-G-A | not specified | Uncertain significance (Dec 17, 2024) | ||
1-109280794-C-T | not specified | Uncertain significance (Mar 08, 2024) | ||
1-109280796-C-T | not specified | Likely benign (May 23, 2023) | ||
1-109280854-G-A | not specified | Uncertain significance (Jun 10, 2024) | ||
1-109280877-T-C | not specified | Likely benign (Jan 17, 2025) | ||
1-109280888-G-A | not specified | Uncertain significance (Jan 02, 2024) | ||
1-109280916-C-T | not specified | Likely benign (Jul 11, 2023) | ||
1-109280974-G-A | not specified | Uncertain significance (Sep 17, 2021) | ||
1-109280978-G-A | not specified | Uncertain significance (Sep 20, 2024) | ||
1-109281001-G-C | not specified | Uncertain significance (Feb 10, 2023) | ||
1-109281010-T-C | not specified | Uncertain significance (Sep 04, 2024) | ||
1-109281019-A-G | not specified | Uncertain significance (Dec 30, 2024) | ||
1-109281155-T-C | not specified | Uncertain significance (Dec 22, 2023) | ||
1-109281172-C-T | not specified | Uncertain significance (Sep 29, 2022) | ||
1-109281173-G-A | not specified | Uncertain significance (Dec 04, 2024) | ||
1-109281176-C-G | not specified | Uncertain significance (Feb 22, 2023) | ||
1-109281197-G-A | not specified | Uncertain significance (Mar 14, 2025) | ||
1-109281212-G-T | not specified | Uncertain significance (Feb 19, 2025) | ||
1-109281223-G-T | not specified | Uncertain significance (Mar 25, 2024) | ||
1-109281627-T-C | not specified | Likely benign (Feb 20, 2025) | ||
1-109281657-G-A | not specified | Uncertain significance (May 16, 2024) | ||
1-109281743-T-G | not specified | Uncertain significance (May 11, 2022) | ||
1-109281791-G-C | not specified | Uncertain significance (May 11, 2022) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
PSRC1 | protein_coding | protein_coding | ENST00000369909 | 7 | 3631 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
8.56e-9 | 0.293 | 125634 | 0 | 114 | 125748 | 0.000453 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.321 | 190 | 203 | 0.937 | 0.0000125 | 2075 |
Missense in Polyphen | 58 | 64.251 | 0.90272 | 706 | ||
Synonymous | -0.488 | 86 | 80.4 | 1.07 | 0.00000444 | 783 |
Loss of Function | 0.653 | 14 | 16.9 | 0.829 | 0.00000134 | 142 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000530 | 0.000530 |
Ashkenazi Jewish | 0.000496 | 0.000496 |
East Asian | 0.0000544 | 0.0000544 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.000257 | 0.000255 |
Middle Eastern | 0.0000544 | 0.0000544 |
South Asian | 0.00194 | 0.00193 |
Other | 0.000653 | 0.000652 |
dbNSFP
Source:
- Function
- FUNCTION: Required for normal progression through mitosis. Required for normal congress of chromosomes at the metaphase plate, and for normal rate of chromosomal segregation during anaphase. Plays a role in the regulation of mitotic spindle dynamics. Increases the rate of turnover of microtubules on metaphase spindles, and contributes to the generation of normal tension across sister kinetochores. Recruits KIF2A and ANKRD53 to the mitotic spindle and spindle poles. May participate in p53/TP53-regulated growth suppression. {ECO:0000269|PubMed:18411309, ECO:0000269|PubMed:19738423, ECO:0000269|PubMed:26820536}.;
- Pathway
- Aryl Hydrocarbon Receptor
(Consensus)
Recessive Scores
- pRec
- 0.0867
Intolerance Scores
- loftool
- 0.308
- rvis_EVS
- 0.71
- rvis_percentile_EVS
- 85.73
Haploinsufficiency Scores
- pHI
- hipred
- N
- hipred_score
- 0.123
- ghis
- 0.449
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.109
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Psrc1
- Phenotype
Gene ontology
- Biological process
- microtubule bundle formation;mitotic metaphase plate congression;negative regulation of cell growth;positive regulation of microtubule polymerization;positive regulation of cyclin-dependent protein serine/threonine kinase activity;positive regulation of transcription, DNA-templated;cell division;regulation of mitotic spindle organization
- Cellular component
- spindle pole;nucleoplasm;cytoplasm;spindle;cytosol;spindle microtubule;microtubule cytoskeleton;midbody
- Molecular function
- protein binding;microtubule binding