PSRC1

proline and serine rich coiled-coil 1

Basic information

Region (hg38): 1:109279555-109283186

Links

ENSG00000134222 ∙ NCBI:84722 ∙ OMIM:613126 ∙ HGNC:24472 ∙ Uniprot:Q6PGN9 ∙ 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 PSRC1 gene.

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			19	2		21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	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)
1-109280794-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)
1-109280888-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)
1-109281001-G-C		not specified	Uncertain significance (Feb 10, 2023)
1-109281155-T-C		not specified	Uncertain significance (Dec 22, 2023)
1-109281172-C-T		not specified	Uncertain significance (Sep 29, 2022)
1-109281176-C-G		not specified	Uncertain significance (Feb 22, 2023)
1-109281212-G-T		not specified	Uncertain significance (Jun 24, 2022)
1-109281223-G-T		not specified	Uncertain significance (Mar 25, 2024)
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)
1-109281818-C-T		not specified	Uncertain significance (Dec 18, 2023)
1-109281852-G-A		not specified	Uncertain significance (May 23, 2024)
1-109281882-C-T		not specified	Uncertain significance (Feb 01, 2023)
1-109281903-C-T		not specified	Uncertain significance (Aug 26, 2022)
1-109282059-G-A			Uncertain significance (Aug 01, 2022)
1-109282520-G-C		not specified	Uncertain significance (Jan 12, 2024)
1-109282548-A-C		not specified	Uncertain significance (Sep 06, 2022)

GnomAD

Source: gnomAD

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: dbNSFP

• 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

• 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

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