PALM

paralemmin, the group of Paralemmins

Basic information

Region (hg38): 19:708935-748329

Links

ENSG00000099864 ∙ NCBI:5064 ∙ OMIM:608134 ∙ HGNC:8594 ∙ Uniprot:O75781 ∙ 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 PALM gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PALM 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			2	44	12	58
missense			92	5	3	100
nonsense			1			1
start loss						0
frameshift						0
inframe indel			1			1
splice donor/acceptor (+/-2bp)						0
splice region			4	7	1	12
non coding				28	11	39
Total	0	0	96	77	26

Variants in PALM

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

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

Position	Type	Phenotype	Significance	ClinVar
19-709160-G-A			Likely benign (Apr 27, 2021)
19-709163-C-G			Likely benign (Jul 19, 2023)
19-709166-T-A			Likely benign (Nov 14, 2022)
19-726128-C-T			Likely benign (Nov 27, 2021)
19-726133-C-T			Likely benign (Aug 17, 2023)
19-726134-G-A			Likely benign (Sep 20, 2022)
19-726146-C-T		not specified	Conflicting classifications of pathogenicity (Nov 27, 2023)
19-726158-C-T			Uncertain significance (Sep 18, 2022)
19-726159-G-A			Likely benign (Jul 06, 2022)
19-726164-A-C			Uncertain significance (Jun 17, 2023)
19-726199-C-T			Likely benign (Jan 15, 2022)
19-726200-G-A			Benign (Jan 22, 2024)
19-726202-C-T			Benign (Oct 03, 2023)
19-726206-C-T			Likely benign (Aug 12, 2021)
19-726207-C-T			Likely benign (Apr 09, 2022)
19-726209-C-T			Likely benign (Oct 23, 2023)
19-726990-A-C			Likely benign (Jan 25, 2024)
19-726994-G-C			Likely benign (Jan 04, 2024)
19-726995-G-T			Likely benign (Aug 23, 2022)
19-726997-C-T			Likely benign (May 16, 2021)
19-726999-T-C			Likely benign (Apr 25, 2023)
19-727002-C-T			Likely benign (Aug 04, 2023)
19-727020-C-T		not specified	Uncertain significance (Jun 24, 2022)
19-727021-G-A		atypical cerebral palsy • not specified	Uncertain significance (Jul 03, 2023)
19-727027-C-T		not specified	Uncertain significance (Feb 23, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PALM	protein_coding	protein_coding	ENST00000338448	9	39377

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.519	0.480	102192	0	1	102193	0.00000489

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.716	223	255	0.874	0.0000180	2445
Missense in Polyphen		63	74.991	0.8401		721
Synonymous	-1.70	144	120	1.20	0.00000980	796
Loss of Function	2.87	3	15.0	0.200	6.40e-7	190

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)	0.0000112	0.0000112
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in plasma membrane dynamics and cell process formation. Isoform 1 and isoform 2 are necessary for axonal and dendritic filopodia induction, for dendritic spine maturation and synapse formation in a palmitoylation-dependent manner. {ECO:0000269|PubMed:14978216}.

Recessive Scores

• pRec: 0.108

Intolerance Scores

• loftool: 0.270
• rvis_EVS: -0.78
• rvis_percentile_EVS: 12.97

Haploinsufficiency Scores

• pHI: 0.0631
• hipred: N
• hipred_score: 0.478
• ghis: 0.588

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.237

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Palm

Gene ontology

• Biological process: cytoskeleton organization;adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway;negative regulation of adenylate cyclase activity;regulation of cell shape;positive regulation of filopodium assembly;synapse maturation;negative regulation of dopamine receptor signaling pathway;cellular response to electrical stimulus;protein localization to plasma membrane
• Cellular component: nucleus;plasma membrane;postsynaptic density;basolateral plasma membrane;apicolateral plasma membrane;axon;intrinsic component of the cytoplasmic side of the plasma membrane;cytoplasmic vesicle;filopodium membrane;dendritic spine membrane;intracellular membrane-bounded organelle
• Molecular function: protein binding;D3 dopamine receptor binding