PRM2

protamine 2

Basic information

Region (hg38): 16:11275639-11276480

Links

ENSG00000122304 ∙ NCBI:5620 ∙ OMIM:182890 ∙ HGNC:9448 ∙ Uniprot:P04554 ∙ 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 PRM2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRM2 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			12	1		13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1	3	4
Total	0	0	12	2	3

Variants in PRM2

This is a list of pathogenic ClinVar variants found in the PRM2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
16-11275896-A-T			Likely benign (Mar 01, 2023)
16-11275916-G-C		not specified	Likely benign (May 18, 2022)
16-11275998-G-T			Benign (Nov 12, 2018)
16-11276073-C-G			Benign (Nov 12, 2018)
16-11276090-G-A			Benign (Jun 26, 2018)
16-11276114-C-T		not specified	Uncertain significance (Feb 10, 2023)
16-11276117-C-T		not specified	Uncertain significance (Mar 29, 2023)
16-11276142-G-A		not specified	Uncertain significance (Apr 26, 2023)
16-11276166-G-C		not specified	Uncertain significance (Oct 08, 2024)
16-11276186-C-G		not specified	Uncertain significance (May 27, 2022)
16-11276210-C-T		not specified	Uncertain significance (Feb 28, 2024)
16-11276250-C-T		not specified	Uncertain significance (Apr 17, 2023)
16-11276277-C-T		not specified	Uncertain significance (Apr 13, 2022)
16-11276311-C-A		not specified	Uncertain significance (Jun 16, 2023)
16-11276340-C-T		not specified	Uncertain significance (May 18, 2022)
16-11276357-C-T		not specified	Uncertain significance (Jan 10, 2023)
16-11276358-G-A		not specified	Uncertain significance (Nov 17, 2023)
16-11276363-C-T		not specified	Uncertain significance (Aug 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PRM2	protein_coding	protein_coding	ENST00000241808	2	842

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0246	0.792	124791	0	9	124800	0.0000361

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.982	96	72.5	1.32	0.00000565	660
Missense in Polyphen		7	5.3107	1.3181		39
Synonymous	-1.06	35	27.9	1.26	0.00000205	193
Loss of Function	0.988	3	5.50	0.546	3.90e-7	42

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.00	0.00
East Asian	0.000111	0.000111
Finnish	0.0000466	0.0000464
European (Non-Finnish)	0.0000443	0.0000441
Middle Eastern	0.000111	0.000111
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Protamines substitute for histones in the chromatin of sperm during the haploid phase of spermatogenesis. They compact sperm DNA into a highly condensed, stable and inactive complex. {ECO:0000250|UniProtKB:P07978}.

Recessive Scores

• pRec: 0.0813

Intolerance Scores

• loftool: 0.313
• rvis_EVS: -0.25
• rvis_percentile_EVS: 35.42

Haploinsufficiency Scores

• pHI: 0.0465
• hipred: N
• hipred_score: 0.146
• ghis: 0.498

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.868

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Prm2
• Phenotype: reproductive system phenotype

Gene ontology

• Biological process: DNA packaging;nucleus organization;multicellular organism development;spermatogenesis;spermatid development;chromosome condensation
• Cellular component: nucleosome;nucleus;nucleoplasm
• Molecular function: DNA binding;zinc ion binding;cadmium ion binding