PRM1

protamine 1

Basic information

Region (hg38): 16:11280840-11281330

Links

ENSG00000175646 ∙ NCBI:5619 ∙ OMIM:182880 ∙ HGNC:9447 ∙ Uniprot:P04553 ∙ 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 PRM1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRM1 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					1	1
missense			8			8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	0	1

Variants in PRM1

This is a list of pathogenic ClinVar variants found in the PRM1 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-11281009-G-T			Benign (Nov 12, 2018)
16-11281141-C-A		not specified	Uncertain significance (Jan 17, 2024)
16-11281142-G-A		not specified	Uncertain significance (Jan 09, 2024)
16-11281165-C-T		not specified	Uncertain significance (Oct 12, 2021)
16-11281171-C-A		not specified	Uncertain significance (Aug 08, 2022)
16-11281198-C-T		not specified	Uncertain significance (Aug 08, 2022)
16-11281205-G-A		not specified	Uncertain significance (May 24, 2023)
16-11281209-C-G		not specified	Uncertain significance (Apr 25, 2022)
16-11281212-G-C		not specified	Uncertain significance (Jun 16, 2024)
16-11281223-A-T		not specified	Uncertain significance (May 23, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PRM1	protein_coding	protein_coding	ENST00000312511	2	515

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0268	0.587	125734	0	3	125737	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.536	45	36.0	1.25	0.00000310	321
Missense in Polyphen		1	2.4254	0.4123		28
Synonymous	-1.60	17	10.4	1.63	5.49e-7	93
Loss of Function	0.0725	2	2.11	0.946	8.93e-8	27

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000578	0.0000578
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	0.0000327	0.0000327
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.

Recessive Scores

• pRec: 0.0368

Intolerance Scores

• loftool: 0.449
• rvis_EVS: 0.35
• rvis_percentile_EVS: 73.97

Haploinsufficiency Scores

• pHI: 0.00810
• hipred: N
• hipred_score: 0.203
• ghis: 0.364

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 5.95e-9

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Prm1
• Phenotype: reproductive system phenotype

Gene ontology

• Biological process: DNA packaging;multicellular organism development;spermatogenesis;cell differentiation;chromosome condensation
• Cellular component: nucleosome;nucleoplasm
• Molecular function: DNA binding