PAMR1

protein-coding

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

Gene summary

Predicted to enable calcium ion binding activity and serine-type endopeptidase activity. Predicted to be involved in proteolysis. Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001001991.3

Inheritance

—

ClinVar variants

U:104B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.11

Max pathogenic AF

—

Genomic locus

chr11:35,431,823-35,530,300

External References & Databases

Ensembl (ENSG00000149090)

Transcript & Mutation Effects

hg38 • Region Span ~98.5 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PAMR1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 101

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001001991.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	1 clinvar		2
missense			102 clinvar	4 clinvar		106
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	104	5	0	109

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 27 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001001991.3	RefSeq	NP_001001991.1	11	MANE Select
ENST00000619888.5	Ensembl	ENSP00000483703.1	11	MANE Select
NM_001282675.2	RefSeq	NP_001269604.1	10	Standard
NM_001282676.2	RefSeq	NP_001269605.1	9	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

calcium ion binding

Cellular Component

extracellular region

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000278360
Coding exons: 12
Length: 98479
Individuals with no LoFs: 125578
Homozygous LoFs: 1
Heterozygous LoFs: 169
Defined: 125748
p: 0.000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.465	460	433	1.06	0.0000248	4801
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00087	0.00086	rare
Latino/Admixed American	0.00052	0.00052	rare
Ashkenazi Jewish	0.0013	0.0013	notable
East Asian	0.00055	0.00054	rare
Finnish	0.00019	0.00018	rare
European (Non-Finnish)	0.00081	0.00080	rare
South Asian	0.00056	0.00052	rare
Other	0.00065	0.00065	rare

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.207

Gene Damage Prediction

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