PALM3

protein-coding

paralemmin 3, the group of Paralemmins

Gene summary

Predicted to enable ATP binding activity. Involved in Toll signaling pathway; negative regulation of cytokine-mediated signaling pathway; and response to lipopolysaccharide. Predicted to be located in cytoplasm and plasma membrane. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001145028.2

Inheritance

—

ClinVar variants

U:107B:10

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.2

Max pathogenic AF

—

Genomic locus

chr19:14,053,363-14,062,076

External References & Databases

Ensembl (ENSG00000187867)

Transcript & Mutation Effects

hg38 • Region Span ~8.7 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 PALM3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 114

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001145028.2. 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			107 clinvar	7 clinvar	1 clinvar	115
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	107	8	2	117

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 11 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001145028.2	RefSeq	NP_001138500.2	7	MANE Select
ENST00000669674.2	Ensembl	ENSP00000499271.1	7	MANE Select
NM_001367327.1	RefSeq	NP_001354256.1	4	Standard
ENST00000340790.9	Ensembl	ENSP00000344996.3	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

negative regulation of cytokine-mediated signaling pathway
Toll signaling pathway
response to lipopolysaccharide

Molecular Function

protein binding
ATP binding

Cellular Component

cytoplasm
plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000340790
Coding exons: 6
Length: 5795
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.32	270	338	0.799	0.0000179	4244
Missense (PolyPhen)		80	94.764	0.8442		1292
Synonymous	2.11	111	143	0.775	0.00000837	1412
Loss of Function	2.38	2	10.2	0.196	6.22e-7	111

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: ATP-binding protein, which may act as a adapter in the Toll-like receptor (TLR) signaling. {ECO:0000269|PubMed:21187075}.;

Intolerance Scores

RVIS EVS: 1.59
RVIS percentile EVS: 95.84

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.231

Gene Damage Prediction

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