PALMD

palmdelphin, the group of Paralemmins

Basic information

Region (hg38): 1:99646113-99694541

Previous symbols: [ "C1orf11" ]

Links

ENSG00000099260 ∙ NCBI:54873 ∙ OMIM:610182 ∙ HGNC:15846 ∙ Uniprot:Q9NP74 ∙ 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 PALMD gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PALMD 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					3	3
missense			38		2	40
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	38	0	5

Variants in PALMD

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

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

Position	Type	Phenotype	Significance	ClinVar
1-99662338-A-C		not specified	Uncertain significance (Sep 01, 2021)
1-99667649-C-T		not specified	Uncertain significance (May 01, 2024)
1-99667681-A-C		not specified	Uncertain significance (Apr 20, 2023)
1-99667734-C-A			Benign (Jul 26, 2018)
1-99667762-C-T		not specified	Uncertain significance (Nov 17, 2022)
1-99686744-T-C		not specified	Uncertain significance (Jan 23, 2024)
1-99686748-G-T		not specified	Uncertain significance (Nov 12, 2021)
1-99686783-T-G		not specified	Uncertain significance (Aug 30, 2022)
1-99688786-A-T		not specified	Uncertain significance (Jan 29, 2024)
1-99688817-C-T		not specified	Uncertain significance (Oct 18, 2021)
1-99688820-G-A		not specified	Uncertain significance (Dec 16, 2021)
1-99688927-A-G		not specified	Uncertain significance (May 20, 2024)
1-99689042-T-C		not specified	Uncertain significance (Jan 31, 2022)
1-99689065-C-T		not specified	Uncertain significance (Jun 17, 2024)
1-99689076-A-T			Benign (Apr 17, 2018)
1-99689093-C-A		not specified	Uncertain significance (Aug 14, 2023)
1-99689117-G-A		not specified	Uncertain significance (Jul 05, 2023)
1-99689147-T-C		not specified	Uncertain significance (Jun 05, 2024)
1-99689222-G-T		not specified	Uncertain significance (Mar 04, 2024)
1-99689249-G-A		not specified	Uncertain significance (Apr 06, 2023)
1-99689257-A-T		not specified	Uncertain significance (Aug 11, 2022)
1-99689321-C-G		not specified	Uncertain significance (Sep 13, 2023)
1-99689324-A-G		not specified	Uncertain significance (Feb 27, 2023)
1-99689392-A-G		not specified	Uncertain significance (Apr 27, 2022)
1-99689428-G-A		not specified	Uncertain significance (Feb 05, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PALMD	protein_coding	protein_coding	ENST00000263174	8	48599

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000339	0.998	125704	0	38	125742	0.000151

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.168	289	281	1.03	0.0000132	3633
Missense in Polyphen		121	113.58	1.0653		1494
Synonymous	-0.822	114	103	1.10	0.00000527	1006
Loss of Function	2.69	10	24.3	0.412	0.00000111	330

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000183	0.000183
Ashkenazi Jewish	0.000298	0.000298
East Asian	0.000164	0.000163
Finnish	0.000140	0.000139
European (Non-Finnish)	0.000106	0.000105
Middle Eastern	0.000164	0.000163
South Asian	0.000392	0.000392
Other	0.000172	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.110

Intolerance Scores

• loftool: 0.673
• rvis_EVS: 0.73
• rvis_percentile_EVS: 86.27

Haploinsufficiency Scores

• pHI: 0.801
• hipred: Y
• hipred_score: 0.544
• ghis: 0.420

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.182

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Palmd

Gene ontology

• Biological process: regulation of cell shape
• Cellular component: cytoplasm;membrane;dendritic spine