PRM3

protamine 3

Basic information

Region (hg38): 16:11273199-11273629

Links

ENSG00000178257 ∙ NCBI:58531 ∙ ∙ HGNC:13732 ∙ Uniprot:Q9NNZ6 ∙ 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 PRM3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRM3 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			16	1	2	19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	16	1	3

Variants in PRM3

This is a list of pathogenic ClinVar variants found in the PRM3 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-11273297-C-T			Benign (Nov 12, 2018)
16-11273303-G-T		not specified	Uncertain significance (May 05, 2023)
16-11273307-C-T		not specified	Uncertain significance (Dec 14, 2024)
16-11273337-T-C		not specified	Likely benign (Nov 17, 2022)
16-11273338-G-C			Benign (Jun 09, 2021)
16-11273347-C-G		not specified	Uncertain significance (Dec 20, 2023)
16-11273384-T-C		not specified	Uncertain significance (Apr 23, 2024)
16-11273395-C-G		not specified	Uncertain significance (Sep 14, 2023)
16-11273412-C-G		not specified	Uncertain significance (Dec 16, 2023)
16-11273418-C-T		not specified	Uncertain significance (Aug 08, 2023)
16-11273419-C-G		not specified	Uncertain significance (Nov 24, 2024)
16-11273423-T-G		not specified	Uncertain significance (Aug 20, 2024)
16-11273450-G-A		not specified	Uncertain significance (Dec 02, 2022)
16-11273471-T-C		not specified	Uncertain significance (Apr 27, 2023)
16-11273490-T-G		not specified	Uncertain significance (Nov 14, 2024)
16-11273525-T-C		not specified	Uncertain significance (Dec 21, 2022)
16-11273546-C-T		not specified	Uncertain significance (Aug 01, 2024)
16-11273558-C-G		not specified	Uncertain significance (Nov 21, 2024)
16-11273585-C-T		not specified	Uncertain significance (Apr 11, 2023)
16-11273586-G-A		not specified	Uncertain significance (Aug 21, 2023)
16-11273620-G-A			Benign (Nov 12, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PRM3	protein_coding	protein_coding	ENST00000327157	1	309

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.360	0.493	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0433	59	59.9	0.984	0.00000360	649
Missense in Polyphen		6	5.9536	1.0078		56
Synonymous	-0.246	30	28.3	1.06	0.00000192	192
Loss of Function	0.780	0	0.709	0.00	2.95e-8	10

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
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 (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.102

Haploinsufficiency Scores

• pHI: 0.187

Essentials

• gene_indispensability_pred: E
• gene_indispensability_score: 0.548

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Prm3
• Phenotype: reproductive system phenotype

Gene ontology

• Biological process: multicellular organism development;spermatogenesis;biological_process;cell differentiation;chromosome condensation;flagellated sperm motility
• Cellular component: nucleosome;cellular_component;nucleus;cytoplasm
• Molecular function: molecular_function;DNA binding