RNF103-CHMP3

RNF103-CHMP3 readthrough

Basic information

Region (hg38): 2:86505668-86721122

Previous symbols: [ "RNF103-VPS24" ]

Links

ENSG00000249884 ∙ NCBI:100526767 ∙ ∙ HGNC:38847 ∙ ∙ ∙ 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 RNF103-CHMP3 gene.

• Inborn genetic diseases (30 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RNF103-CHMP3 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			7			7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			23			23
Total	0	0	30	0	0

Variants in RNF103-CHMP3

This is a list of pathogenic ClinVar variants found in the RNF103-CHMP3 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-86505929-T-C		not specified	Uncertain significance (May 17, 2023)
2-86507545-C-T		not specified	Uncertain significance (Apr 22, 2022)
2-86507546-G-T		not specified	Uncertain significance (Oct 29, 2021)
2-86510390-T-C		not specified	Uncertain significance (Nov 11, 2024)
2-86529254-T-C		not specified	Uncertain significance (Sep 14, 2023)
2-86529271-T-C		not specified	Uncertain significance (Mar 08, 2024)
2-86529349-G-A		not specified	Uncertain significance (Jan 31, 2022)
2-86529355-T-C		not specified	Uncertain significance (Feb 26, 2025)
2-86529365-A-C		not specified	Uncertain significance (Nov 18, 2022)
2-86529388-C-G		not specified	Uncertain significance (Sep 29, 2023)
2-86542289-T-C		not specified	Uncertain significance (Mar 07, 2024)
2-86542306-C-T		not specified	Uncertain significance (Apr 05, 2023)
2-86563309-C-T		not specified	Uncertain significance (Jul 14, 2023)
2-86603934-C-T		not specified	Uncertain significance (Jan 26, 2023)
2-86604013-T-C		not specified	Uncertain significance (Jul 27, 2024)
2-86604023-C-A		not specified	Uncertain significance (Jun 25, 2024)
2-86604082-C-T		not specified	Uncertain significance (Jan 21, 2025)
2-86604086-T-G		not specified	Uncertain significance (Sep 27, 2021)
2-86604087-T-C		not specified	Uncertain significance (May 24, 2023)
2-86604093-T-A		not specified	Uncertain significance (Oct 25, 2024)
2-86604177-G-A		not specified	Uncertain significance (Aug 15, 2023)
2-86604285-G-C		not specified	Uncertain significance (Mar 16, 2022)
2-86604287-G-C		not specified	Uncertain significance (Nov 11, 2024)
2-86604297-G-C		not specified	Uncertain significance (Sep 11, 2024)
2-86604306-G-A		not specified	Uncertain significance (Dec 03, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RNF103-CHMP3	protein_coding	protein_coding	ENST00000604011	6	215455

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00400	0.963	125736	0	12	125748	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.801	108	134	0.805	0.00000649	1668
Missense in Polyphen		12	22.037	0.54454		282
Synonymous	0.984	36	44.3	0.812	0.00000225	434
Loss of Function	1.86	6	13.3	0.450	7.38e-7	163

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000877	0.0000877
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.0000448	0.0000439
Middle Eastern	0.000163	0.000163
South Asian	0.00	0.00
Other	0.000176	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable core component of the endosomal sorting required for transport complex III (ESCRT-III) which is involved in multivesicular bodies (MVBs) formation and sorting of endosomal cargo proteins into MVBs. MVBs contain intraluminal vesicles (ILVs) that are generated by invagination and scission from the limiting membrane of the endosome and mostly are delivered to lysosomes enabling degradation of membrane proteins, such as stimulated growth factor receptors, lysosomal enzymes and lipids. The MVB pathway appears to require the sequential function of ESCRT-O, -I,-II and -III complexes. ESCRT-III proteins mostly dissociate from the invaginating membrane before the ILV is released. The ESCRT machinery also functions in topologically equivalent membrane fission events, such as the terminal stages of cytokinesis and the budding of enveloped viruses (HIV-1 and other lentiviruses). ESCRT-III proteins are believed to mediate the necessary vesicle extrusion and/or membrane fission activities, possibly in conjunction with the AAA ATPase VPS4. Selectively binds to phosphatidylinositol 3,5-bisphosphate PtdIns(3,5)P2 and PtdIns(3,4)P2 in preference to other phosphoinositides tested. Involved in late stages of cytokinesis. Plays a role in endosomal sorting/trafficking of EGF receptor. Isoform 2 prevents stress- mediated cell death and accumulation of reactive oxygen species when expressed in yeast cells. {ECO:0000269|PubMed:14505570, ECO:0000269|PubMed:15707591, ECO:0000269|PubMed:16740483, ECO:0000269|PubMed:17331679, ECO:0000269|PubMed:18076377}.
• Pathway: Endocytosis - Homo sapiens (human);Necroptosis - Homo sapiens (human);Disease;Vesicle-mediated transport;Membrane Trafficking;Budding and maturation of HIV virion;Late Phase of HIV Life Cycle;HIV Life Cycle;HIV Infection;Endosomal Sorting Complex Required For Transport (ESCRT);Infectious disease;Internalization of ErbB1 (Consensus)

Intolerance Scores

• rvis_EVS: -0.38
• rvis_percentile_EVS: 27.42

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.172
• ghis: 0.411

Essentials

• essential_gene_CRISPR: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene ontology

• Biological process: vacuolar transport