STOML3

stomatin like 3, the group of Stomatin family

Basic information

Region (hg38): 13:38965925-38990859

Links

ENSG00000133115 ∙ ∙ OMIM:608327 ∙ HGNC:19420 ∙ Uniprot:Q8TAV4 ∙ 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 STOML3 gene.

• not_specified (52 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the STOML3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000145286.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			51	1		52
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	51	1	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
STOML3	protein_coding	protein_coding	ENST00000379631	7	25142

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.58e-14	0.00497	125476	1	271	125748	0.00108

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.372	185	171	1.08	0.00000985	1860
Missense in Polyphen		80	79.902	1.0012		837
Synonymous	1.06	56	67.0	0.835	0.00000376	609
Loss of Function	-0.735	19	15.8	1.20	9.42e-7	163

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00158	0.00158
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000231	0.000231
European (Non-Finnish)	0.00173	0.00172
Middle Eastern	0.00	0.00
South Asian	0.000623	0.000588
Other	0.000490	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for the function of many mechanoreceptors. Modulate mechanotransduction channels and acid-sensing ion channels (ASIC) proteins. Potentiates PIEZO1 and PIEZO2 function by increasing their sensitivity to mechanical stimulations. {ECO:0000250|UniProtKB:Q6PE84}.
• Pathway: Stimuli-sensing channels;Ion channel transport;Transport of small molecules (Consensus)

Recessive Scores

• pRec: 0.127

Intolerance Scores

• loftool: 0.218
• rvis_EVS: 0.46
• rvis_percentile_EVS: 78.59

Haploinsufficiency Scores

• pHI: 0.194
• hipred: N
• hipred_score: 0.197

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.307

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Stoml3
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan)

Gene ontology

• Biological process: signal transduction;biological_process;ion transmembrane transport
• Cellular component: cellular_component;plasma membrane;cilium;integral component of membrane;membrane raft
• Molecular function: molecular_function