PLEKHM3

pleckstrin homology domain containing M3, the group of Pleckstrin homology domain containing

Basic information

Region (hg38): 2:207821288-208025527

Previous symbols: [ "PLEKHM1L" ]

Links

ENSG00000178385 ∙ NCBI:389072 ∙ OMIM:619186 ∙ HGNC:34006 ∙ Uniprot:Q6ZWE6 ∙ 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 PLEKHM3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLEKHM3 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						0
missense			36			36
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	36	0	0

Variants in PLEKHM3

This is a list of pathogenic ClinVar variants found in the PLEKHM3 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-207828443-G-C		not specified	Uncertain significance (Jan 09, 2024)
2-207828450-A-G		not specified	Uncertain significance (Apr 06, 2024)
2-207861107-G-C		not specified	Uncertain significance (Jan 03, 2024)
2-207861111-G-A		not specified	Uncertain significance (Mar 30, 2024)
2-207861116-A-C		not specified	Uncertain significance (Jan 04, 2022)
2-207861117-A-G		not specified	Uncertain significance (Dec 27, 2023)
2-207861130-G-A		not specified	Uncertain significance (Nov 12, 2021)
2-207861153-C-T		not specified	Uncertain significance (Dec 19, 2022)
2-207861202-C-T		not specified	Uncertain significance (Mar 29, 2024)
2-207861255-T-C		not specified	Uncertain significance (Nov 22, 2023)
2-207931019-A-C		not specified	Uncertain significance (Apr 04, 2023)
2-207946402-G-A		not specified	Uncertain significance (Jan 27, 2022)
2-207946437-C-T		not specified	Uncertain significance (Aug 23, 2021)
2-207946477-C-T		not specified	Uncertain significance (Dec 20, 2023)
2-207946509-C-A		not specified	Uncertain significance (Feb 03, 2022)
2-207976701-G-A		not specified	Uncertain significance (Dec 07, 2023)
2-207976731-G-C		not specified	Uncertain significance (Mar 20, 2023)
2-207976740-T-C		not specified	Uncertain significance (Mar 15, 2024)
2-207976764-C-T		not specified	Uncertain significance (Feb 14, 2023)
2-207976776-T-C		not specified	Uncertain significance (Apr 13, 2022)
2-207976777-T-C		not specified	Uncertain significance (Jun 21, 2022)
2-207976789-T-C		not specified	Uncertain significance (Apr 20, 2024)
2-207976855-T-A		not specified	Uncertain significance (Jun 02, 2023)
2-207976867-C-T		not specified	Uncertain significance (Sep 28, 2022)
2-207976875-C-T		not specified	Uncertain significance (Jan 18, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PLEKHM3	protein_coding	protein_coding	ENST00000427836	7	197258

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000100	1.00	124778	0	27	124805	0.000108

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.45	343	428	0.802	0.0000240	5018
Missense in Polyphen		121	164.08	0.73743		1893
Synonymous	1.06	154	172	0.897	0.00000998	1445
Loss of Function	3.68	14	38.7	0.362	0.00000235	392

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000541	0.000539
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000556	0.0000556
Finnish	0.0000928	0.0000928
European (Non-Finnish)	0.0000974	0.0000971
Middle Eastern	0.0000556	0.0000556
South Asian	0.0000327	0.0000327
Other	0.000330	0.000330

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in skeletal muscle differentiation. May act as a scaffold protein for AKT1 during muscle differentiation. {ECO:0000250|UniProtKB:Q8BM47}.

Intolerance Scores

• loftool: 0.266
• rvis_EVS: 0.02
• rvis_percentile_EVS: 55.61

Haploinsufficiency Scores

• pHI: 0.340
• hipred: N
• hipred_score: 0.488
• ghis: 0.468

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.451

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Plekhm3

Gene ontology

• Biological process: myoblast differentiation
• Cellular component: cytoplasm;Golgi apparatus;plasma membrane
• Molecular function: metal ion binding