PSRC1

protein-coding

proline and serine rich coiled-coil 1

Gene summary

This gene encodes a proline-rich protein that is a target for regulation by the tumor suppressor protein p53. The encoded protein plays an important role in mitosis by recruiting and regulating microtubule depolymerases that destabalize microtubules. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Apr 2014]

MANE transcript

NM_001032291.3

Inheritance

—

ClinVar variants

U:50B:8

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.83

Max pathogenic AF

—

Genomic locus

chr1:109,279,556-109,283,186

External References & Databases

Ensembl (ENSG00000134222)

Transcript & Mutation Effects

hg38 • Region Span ~3.6 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PSRC1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 55

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001032291.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				4 clinvar		4
missense			50 clinvar	4 clinvar		54
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	50	8	0	58

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 148 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001032291.3	RefSeq	NP_001027462.1	7	MANE Select
ENST00000369909.7	Ensembl	ENSP00000358925.2	7	MANE Select
NM_001005290.4	RefSeq	NP_001005290.1	7	Standard
NM_001350237.2	RefSeq	NP_001337166.1	7	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Aryl Hydrocarbon Receptor

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

Molecular Function

protein binding
microtubule binding

Cellular Component

spindle pole
nucleoplasm
cytoplasm
spindle
cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000369909
Coding exons: 7
Length: 3631
Individuals with no LoFs: 125634
Homozygous LoFs: 0
Heterozygous LoFs: 114
Defined: 125748
p: 0.000453

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.321	190	203	0.937	0.0000125	2075
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.00041	0.00040	rare
Ashkenazi Jewish	0.00050	0.00050	rare
East Asian	0.000054	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00026	0.00025	rare
South Asian	0.0019	0.0019	notable
Other	0.00065	0.00065	rare

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.0867

Intolerance Scores

LoFtool: 0.308
RVIS EVS: 0.71
RVIS percentile EVS: 85.73

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.109

Gene Damage Prediction

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