PAMR1

peptidase domain containing associated with muscle regeneration 1, the group of Sushi domain containing

Basic information

Region (hg38): 11:35431823-35530300

Links

ENSG00000149090 ∙ NCBI:25891 ∙ ∙ HGNC:24554 ∙ Uniprot:Q6UXH9 ∙ 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 PAMR1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PAMR1 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			44	2		46
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	44	3	0

Variants in PAMR1

This is a list of pathogenic ClinVar variants found in the PAMR1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-35432377-C-A		not specified	Uncertain significance (Jan 18, 2022)
11-35432478-G-A		not specified	Uncertain significance (Aug 19, 2023)
11-35432498-G-A		not specified	Uncertain significance (Nov 21, 2023)
11-35432513-G-A		not specified	Uncertain significance (Oct 17, 2023)
11-35432519-C-T		not specified	Uncertain significance (May 29, 2024)
11-35432594-C-T		not specified	Uncertain significance (Aug 13, 2021)
11-35432617-A-G			Likely benign (Aug 01, 2022)
11-35432666-C-T		not specified	Uncertain significance (Oct 10, 2023)
11-35432667-G-A		not specified	Uncertain significance (Dec 14, 2021)
11-35432700-C-T		not specified	Uncertain significance (Mar 20, 2024)
11-35432765-C-T		not specified	Uncertain significance (Sep 27, 2021)
11-35432798-G-A		not specified	Uncertain significance (Jan 16, 2024)
11-35432807-C-T		not specified	Uncertain significance (Jul 25, 2023)
11-35432808-G-A		not specified	Uncertain significance (Jun 11, 2021)
11-35434550-C-T		not specified	Uncertain significance (May 10, 2024)
11-35434552-C-T		not specified	Uncertain significance (Sep 13, 2023)
11-35434568-A-C		not specified	Uncertain significance (Nov 10, 2022)
11-35434598-T-C		not specified	Likely benign (Mar 16, 2022)
11-35434718-C-T		not specified	Uncertain significance (Aug 13, 2021)
11-35434756-C-T		not specified	Uncertain significance (Nov 17, 2023)
11-35435923-C-T		not specified	Uncertain significance (Aug 19, 2023)
11-35435924-G-A		not specified	Uncertain significance (Jun 13, 2022)
11-35435950-C-T		not specified	Uncertain significance (Jan 17, 2024)
11-35435974-C-T		not specified	Uncertain significance (Dec 16, 2023)
11-35435978-G-A		not specified	Uncertain significance (Mar 15, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PAMR1	protein_coding	protein_coding	ENST00000278360	12	98479

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.26e-32	0.00000527	125578	1	169	125748	0.000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.465	460	433	1.06	0.0000248	4801
Missense in Polyphen		220	192.32	1.144		2205
Synonymous	-0.381	174	168	1.04	0.00000985	1429
Loss of Function	-0.677	45	40.4	1.11	0.00000251	412

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00139	0.00138
Ashkenazi Jewish	0.00129	0.00129
East Asian	0.000551	0.000544
Finnish	0.000185	0.000185
European (Non-Finnish)	0.000805	0.000800
Middle Eastern	0.000551	0.000544
South Asian	0.000564	0.000523
Other	0.000654	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in regeneration of skeletal muscle. {ECO:0000250}.

Intolerance Scores

• rvis_EVS: -0.5
• rvis_percentile_EVS: 21.84

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.350
• ghis: 0.497

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.207

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pamr1

Gene ontology

• Cellular component: extracellular region
• Molecular function: calcium ion binding