RAB5IF

RAB5 interacting factor

Basic information

Region (hg38): 20:36605779-36612557

Previous symbols: [ "C20orf24" ]

Links

ENSG00000101084 ∙ NCBI:55969 ∙ OMIM:619960 ∙ HGNC:15870 ∙ Uniprot:Q9BUV8 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• craniofacial dysmorphism, skeletal anomalies, and impaired intellectual development syndrome 2 (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Craniofacial dysmorphism, skeletal anomalies, and impaired intellectual development syndrome 2	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Craniofacial; Musculoskeletal; Neurologic	35614220

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RAB5IF gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RAB5IF 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			1			1
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	2	0	0

Variants in RAB5IF

This is a list of pathogenic ClinVar variants found in the RAB5IF region.

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

Position	Type	Phenotype	Significance	ClinVar
20-36606026-G-A		Craniofacial dysmorphism, skeletal anomalies, and impaired intellectual development syndrome 2 • 10 conditions • Craniofacial dysmorphism, skeletal anomalies, and impaired intellectual development 1	Pathogenic/Likely pathogenic (Jun 01, 2021)
20-36606060-G-A		not specified	Uncertain significance (Aug 17, 2021)
20-36612149-T-A		not specified	Uncertain significance (Oct 26, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RAB5IF	protein_coding	protein_coding	ENST00000342422	3	6824

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.670	0.326	125730	0	18	125748	0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.509	60	72.2	0.831	0.00000384	896
Missense in Polyphen		11	18.34	0.59978		232
Synonymous	-1.72	40	28.3	1.41	0.00000144	298
Loss of Function	2.27	1	7.89	0.127	5.25e-7	73

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000145	0.000145
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.00000879	0.00000879
Middle Eastern	0.0000544	0.0000544
South Asian	0.000359	0.000359
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: -0.23
• rvis_percentile_EVS: 36.86

Haploinsufficiency Scores

• pHI: 0.0776
• hipred: N
• hipred_score: 0.252
• ghis: 0.493

Essentials

• essential_gene_gene_trap: K

Mouse Genome Informatics

• Gene name: Rab5if

Gene ontology

• Biological process: biological_process
• Cellular component: cellular_component
• Molecular function: molecular_function