PARM1

prostate androgen-regulated mucin-like protein 1

Basic information

Region (hg38): 4:74933095-75050115

Links

ENSG00000169116 ∙ NCBI:25849 ∙ OMIM:617688 ∙ HGNC:24536 ∙ Uniprot:Q6UWI2 ∙ 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 PARM1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PARM1 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			9	1	1	11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	1	1

Variants in PARM1

This is a list of pathogenic ClinVar variants found in the PARM1 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-74933331-G-T		not specified	Uncertain significance (Dec 15, 2022)
4-75012653-C-G		not specified	Uncertain significance (Sep 14, 2022)
4-75012685-A-T		not specified	Uncertain significance (Jan 26, 2022)
4-75012695-C-T		not specified	Uncertain significance (May 27, 2022)
4-75012704-G-C			Benign (Jul 26, 2018)
4-75012719-G-A		not specified	Uncertain significance (Aug 10, 2024)
4-75012797-C-T		not specified	Uncertain significance (May 01, 2024)
4-75012805-G-A		not specified	Uncertain significance (Dec 06, 2021)
4-75012883-G-A		not specified	Uncertain significance (Aug 05, 2024)
4-75012898-G-A		not specified	Likely benign (Aug 02, 2021)
4-75012916-T-C		not specified	Uncertain significance (Jun 28, 2024)
4-75012932-C-T		not specified	Uncertain significance (Apr 07, 2022)
4-75012962-A-T		not specified	Uncertain significance (Apr 24, 2024)
4-75012983-G-A		not specified	Likely benign (Oct 19, 2024)
4-75012984-C-A		not specified	Uncertain significance (Oct 19, 2024)
4-75013018-G-A		not specified	Uncertain significance (Sep 30, 2024)
4-75013043-C-G		not specified	Uncertain significance (Aug 02, 2021)
4-75013066-G-A		not specified	Uncertain significance (Sep 14, 2022)
4-75013094-C-A		not specified	Uncertain significance (Sep 16, 2021)
4-75033897-A-C		not specified	Uncertain significance (Dec 04, 2024)
4-75033900-A-C		not specified	Uncertain significance (Dec 04, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PARM1	protein_coding	protein_coding	ENST00000307428	4	117021

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000869	0.806	124626	0	55	124681	0.000221

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0738	162	165	0.984	0.00000861	1948
Missense in Polyphen		26	38.338	0.67818		476
Synonymous	-1.40	88	72.8	1.21	0.00000484	695
Loss of Function	1.11	6	9.74	0.616	4.20e-7	128

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.000222	0.000222
Finnish	0.00195	0.00195
European (Non-Finnish)	0.0000714	0.0000619
Middle Eastern	0.000222	0.000222
South Asian	0.0000658	0.0000654
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May regulate TLP1 expression and telomerase activity, thus enabling certain prostatic cells to resist apoptosis. {ECO:0000250}.

Intolerance Scores

• loftool: 0.505
• rvis_EVS: 0.6
• rvis_percentile_EVS: 82.74

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.123
• ghis: 0.404

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.231

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Parm1

Gene ontology

• Biological process: positive regulation of telomerase activity
• Cellular component: Golgi membrane;nucleus;early endosome;late endosome;Golgi apparatus;cytosol;plasma membrane;endosome membrane;integral component of membrane;intracellular membrane-bounded organelle