ISY1-RAB43

ISY1-RAB43 readthrough

Basic information

Region (hg38): 3:129087575-129161036

Links

ENSG00000261796 ∙ NCBI:100534599 ∙ ∙ HGNC:42969 ∙ ∙ ∙ 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 ISY1-RAB43 gene.

• Inborn genetic diseases (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ISY1-RAB43 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						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			3			3
Total	0	0	3	0	0

Variants in ISY1-RAB43

This is a list of pathogenic ClinVar variants found in the ISY1-RAB43 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-129091125-T-C		not specified	Likely benign (Dec 15, 2023)
3-129091194-T-C		not specified	Likely benign (Jan 16, 2024)
3-129091202-G-A		not specified	Uncertain significance (Oct 05, 2022)
3-129091226-T-G		not specified	Uncertain significance (Oct 11, 2024)
3-129091231-G-C		not specified	Uncertain significance (Sep 02, 2024)
3-129091289-A-G		not specified	Uncertain significance (May 30, 2023)
3-129092570-G-C		RAB43-related disorder	Uncertain significance (Jan 22, 2024)
3-129092596-A-C		RAB43-related disorder	Likely benign (Mar 08, 2022)
3-129094987-G-A		RAB43-related disorder	Likely benign (Feb 23, 2022)
3-129095014-C-T		RAB43-related disorder	Likely benign (Feb 01, 2023)
3-129095017-A-G		RAB43-related disorder	Likely benign (Dec 27, 2022)
3-129121293-C-A		not specified	Uncertain significance (Jan 04, 2024)
3-129121432-T-C		not specified	Uncertain significance (Jul 09, 2024)
3-129121439-G-A		RAB43-related disorder	Likely benign (Mar 22, 2022)
3-129121478-C-T		RAB43-related disorder	Benign (Jun 02, 2022)
3-129121480-G-C		not specified	Uncertain significance (Aug 26, 2024)
3-129134150-C-G		not specified	Uncertain significance (Mar 20, 2024)
3-129137140-C-T		not specified	Uncertain significance (May 18, 2023)
3-129137145-G-A		not specified	Uncertain significance (Apr 08, 2024)
3-129137150-A-G		EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)
3-129137164-C-T		not specified	Uncertain significance (Mar 14, 2024)
3-129137192-C-G		not specified	Uncertain significance (Jul 05, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ISY1-RAB43	protein_coding	protein_coding	ENST00000418265	12	73462

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000304	125737	0	5	125742	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.42	135	190	0.711	0.0000109	2120
Missense in Polyphen		33	63.794	0.51729		741
Synonymous	2.11	47	69.4	0.677	0.00000422	629
Loss of Function	4.69	1	27.6	0.0362	0.00000188	284

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000302	0.0000302
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000880	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.0000982	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in pre-mRNA splicing as component of the spliceosome. {ECO:0000305|PubMed:11991638, ECO:0000305|PubMed:25599396}.
• Pathway: Spliceosome - Homo sapiens (human);DNA Repair;Metabolism of RNA;mRNA Splicing - Major Pathway;Formation of TC-NER Pre-Incision Complex;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA;Dual incision in TC-NER;Gap-filling DNA repair synthesis and ligation in TC-NER;Transcription-Coupled Nucleotide Excision Repair (TC-NER);Nucleotide Excision Repair (Consensus)

Intolerance Scores

• rvis_EVS: -0.19
• rvis_percentile_EVS: 39.68

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.380
• ghis: 0.413

Essentials

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

Gene Damage Prediction

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