PRIM2

DNA primase subunit 2, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 6:57314805-57646850

Previous symbols: [ "PRIM2A" ]

Links

ENSG00000146143

∙ NCBI:5558 ∙ OMIM:176636 ∙ HGNC:9370 ∙ Uniprot:P49643 ∙ 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 PRIM2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRIM2 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						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	0	0	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PRIM2	protein_coding	protein_coding	ENST00000607273	10	333773

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.16e-7	0.804	124586	0	66	124652	0.000265

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.755	125	151	0.827	0.00000718	2121
Missense in Polyphen		28	51.787	0.54067		727
Synonymous	3.00	24	51.4	0.467	0.00000225	552
Loss of Function	1.44	14	21.2	0.661	0.00000120	260

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00184	0.00179
Ashkenazi Jewish	0.00	0.00
East Asian	0.000375	0.000334
Finnish	0.0000994	0.0000928
European (Non-Finnish)	0.000129	0.000106
Middle Eastern	0.000375	0.000334
South Asian	0.000200	0.000196
Other	0.000378	0.000330

dbNSFP

Source: dbNSFP

Function: FUNCTION: DNA primase is the polymerase that synthesizes small RNA primers for the Okazaki fragments made during discontinuous DNA replication.;
Pathway: Pyrimidine metabolism - Homo sapiens (human);DNA replication - Homo sapiens (human);Purine metabolism - Homo sapiens (human);Pyrimidine metabolism;G1 to S cell cycle control;DNA Replication;Inhibition of replication initiation of damaged DNA by RB1/E2F1;Polymerase switching on the C-strand of the telomere;Activation of the pre-replicative complex;E2F mediated regulation of DNA replication;Mitotic G1-G1/S phases;DNA replication initiation;DNA Replication;Polymerase switching;Leading Strand Synthesis;Removal of the Flap Intermediate;Processive synthesis on the lagging strand;Lagging Strand Synthesis;DNA strand elongation;Synthesis of DNA;S Phase;Telomere C-strand synthesis initiation;Telomere C-strand (Lagging Strand) Synthesis;Extension of Telomeres;Telomere Maintenance;Chromosome Maintenance;G1/S Transition;DNA Replication Pre-Initiation;M/G1 Transition;Cell Cycle;Cell Cycle, Mitotic (Consensus)

Recessive Scores

pRec: 0.0831

Haploinsufficiency Scores

pHI: 0.892
hipred: N
hipred_score: 0.216
ghis

Essentials

essential_gene_CRISPR
essential_gene_CRISPR2
essential_gene_gene_trap
gene_indispensability_pred: N
gene_indispensability_score: 0.000118

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Prim2
Phenotype

Gene ontology

Biological process: G1/S transition of mitotic cell cycle;DNA replication, synthesis of RNA primer;telomere maintenance via semi-conservative replication
Cellular component: nucleoplasm;alpha DNA polymerase:primase complex
Molecular function: single-stranded DNA binding;DNA primase activity;metal ion binding;4 iron, 4 sulfur cluster binding