PALM3

paralemmin 3, the group of Paralemmins

Basic information

Region (hg38): 19:14053362-14062076

Links

ENSG00000187867 ∙ NCBI:342979 ∙ ∙ HGNC:33274 ∙ Uniprot:A6NDB9 ∙ 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 PALM3 gene.

• Inborn genetic diseases (32 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PALM3 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			29	3	1	33
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	29	3	2

Variants in PALM3

This is a list of pathogenic ClinVar variants found in the PALM3 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-14053613-C-G		not specified	Uncertain significance (Jun 11, 2021)
19-14053615-G-A		not specified	Uncertain significance (Jun 17, 2022)
19-14053633-T-C		not specified	Uncertain significance (Aug 30, 2022)
19-14053733-C-T		not specified	Uncertain significance (Feb 28, 2024)
19-14053805-G-A		not specified	Uncertain significance (Jan 19, 2024)
19-14053845-G-A			Benign (Nov 20, 2018)
19-14053853-G-A		not specified	Uncertain significance (Apr 25, 2023)
19-14053907-C-T		not specified	Uncertain significance (Aug 14, 2023)
19-14053945-G-A		not specified	Uncertain significance (Aug 02, 2021)
19-14054026-G-A		not specified	Uncertain significance (Dec 15, 2022)
19-14054072-T-C		not specified	Uncertain significance (Dec 03, 2021)
19-14054161-T-C		not specified	Uncertain significance (May 24, 2023)
19-14054203-C-T		not specified	Uncertain significance (Jul 26, 2021)
19-14054287-C-T		not specified	Uncertain significance (Jan 30, 2024)
19-14054308-G-A		not specified	Uncertain significance (Dec 28, 2022)
19-14054341-T-C		not specified	Uncertain significance (Feb 05, 2024)
19-14054395-C-G		not specified	Uncertain significance (Jun 29, 2023)
19-14054432-C-T		not specified	Uncertain significance (Mar 04, 2024)
19-14054434-G-A		not specified	Uncertain significance (May 31, 2023)
19-14054459-T-C		not specified	Uncertain significance (Feb 07, 2023)
19-14054465-C-T		not specified	Uncertain significance (Dec 28, 2023)
19-14054476-G-A		not specified	Uncertain significance (Jun 10, 2022)
19-14054542-T-A		not specified	Uncertain significance (Mar 08, 2024)
19-14054734-A-G		not specified	Likely benign (Nov 19, 2022)
19-14054741-G-A		not specified	Uncertain significance (Dec 07, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PALM3	protein_coding	protein_coding	ENST00000340790	6	5795

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.484	0.511	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.32	270	338	0.799	0.0000179	4244
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

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_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: Palm3

Gene ontology

• Biological process: negative regulation of cytokine-mediated signaling pathway;Toll signaling pathway;response to lipopolysaccharide
• Cellular component: cytoplasm;plasma membrane
• Molecular function: protein binding;ATP binding