STOML1

stomatin like 1, the group of Stomatin family

Basic information

Region (hg38): 15:73978926-73994622

Links

ENSG00000067221 ∙ NCBI:9399 ∙ OMIM:608326 ∙ HGNC:14560 ∙ Uniprot:Q9UBI4 ∙ 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 STOML1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the STOML1 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			28	1		29
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	28	1	0

Variants in STOML1

This is a list of pathogenic ClinVar variants found in the STOML1 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-73983972-T-C		not specified	Uncertain significance (Jan 30, 2024)
15-73983987-C-T		not specified	Uncertain significance (Jun 11, 2021)
15-73984055-C-T		not specified	Likely benign (Aug 10, 2023)
15-73984056-G-A		not specified	Uncertain significance (Feb 15, 2025)
15-73984076-T-A		not specified	Uncertain significance (Mar 16, 2024)
15-73984085-A-G		not specified	Uncertain significance (Jul 05, 2022)
15-73984110-C-T		not specified	Uncertain significance (Jan 08, 2025)
15-73984683-C-T		not specified	Uncertain significance (Jun 11, 2024)
15-73984731-C-T		not specified	Uncertain significance (Jan 30, 2025)
15-73984752-C-T		not specified	Uncertain significance (Dec 21, 2023)
15-73984829-G-A		not specified	Uncertain significance (Jan 04, 2024)
15-73984854-C-T		not specified	Uncertain significance (Mar 06, 2023)
15-73984865-G-A		not specified	Uncertain significance (Mar 19, 2024)
15-73985323-C-A		not specified	Uncertain significance (Mar 15, 2024)
15-73985326-G-A		not specified	Uncertain significance (Nov 21, 2023)
15-73985368-A-G		not specified	Uncertain significance (Nov 28, 2024)
15-73985468-G-A		not specified	Uncertain significance (Sep 27, 2024)
15-73985501-C-T		not specified	Uncertain significance (Dec 17, 2021)
15-73985504-T-C		not specified	Uncertain significance (Feb 22, 2023)
15-73988610-C-T		not specified	Uncertain significance (Feb 07, 2025)
15-73988616-T-G		not specified	Uncertain significance (Feb 01, 2025)
15-73988648-G-A		not specified	Uncertain significance (Feb 22, 2023)
15-73988673-T-C		not specified	Uncertain significance (Jan 24, 2024)
15-73988691-T-C		not specified	Uncertain significance (Dec 19, 2023)
15-73988693-C-T		not specified	Uncertain significance (Mar 01, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
STOML1	protein_coding	protein_coding	ENST00000316900	7	11417

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.42e-11	0.0388	125712	0	36	125748	0.000143

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.43	174	236	0.738	0.0000140	2531
Missense in Polyphen		25	41.789	0.59824		481
Synonymous	1.24	89	105	0.846	0.00000648	872
Loss of Function	-0.134	16	15.4	1.04	8.57e-7	163

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000424	0.000423
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000152	0.000149
Middle Eastern	0.000109	0.000109
South Asian	0.000229	0.000229
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in cholesterol transfer to late endosomes (PubMed:19696025). May play a role in modulating membrane acid-sensing ion channels. Can specifically inhibit proton-gated current of ASIC1 isoform 1. Can increase inactivation speed of ASIC3. May be involved in regulation of proton sensing in dorsal root ganglions (By similarity). May play a role in protecting FBXW7 isoform 3 from degradation (PubMed:23082202). {ECO:0000250|UniProtKB:Q8CI66, ECO:0000269|PubMed:19696025, ECO:0000305|PubMed:23082202}.

Recessive Scores

• pRec: 0.149

Intolerance Scores

• loftool: 0.356
• rvis_EVS: -0.4
• rvis_percentile_EVS: 26.73

Haploinsufficiency Scores

• pHI: 0.235
• hipred: N
• hipred_score: 0.335
• ghis: 0.648

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.787

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Stoml1
• Phenotype: 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)

Gene ontology

• Biological process: lipid transport;biological_process
• Cellular component: cellular_component;plasma membrane;integral component of membrane;late endosome membrane;membrane raft
• Molecular function: molecular_function;protein binding