TGIF2-RAB5IF

TGIF2-RAB5IF readthrough

Basic information

Region (hg38): 20:36574553-36612384

Previous symbols: [ "TGIF2-C20orf24" ]

Links

ENSG00000259399 ∙ NCBI:100527943 ∙ ∙ HGNC:44664 ∙ ∙ ∙ 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 TGIF2-RAB5IF gene.

• Inborn genetic diseases (6 variants)
• Craniofacial dysmorphism, skeletal anomalies, and impaired intellectual development syndrome 2 (1 variants)
• Craniofacial dysmorphism, skeletal anomalies, and impaired intellectual development 1 (1 variants)
• 10 conditions (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TGIF2-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	5			6
Total	0	1	6	0	0

Variants in TGIF2-RAB5IF

This is a list of pathogenic ClinVar variants found in the TGIF2-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
20-36578802-G-A		not specified	Uncertain significance (Mar 06, 2023)
20-36590980-C-A		not specified	Uncertain significance (Mar 28, 2023)
20-36591004-G-A		not specified	Uncertain significance (Dec 06, 2022)
20-36591028-C-T		not specified	Uncertain significance (Sep 01, 2021)
20-36591054-G-A		not specified	Uncertain significance (Mar 01, 2023)
20-36591097-T-A		not specified	Uncertain significance (Apr 15, 2024)
20-36591177-C-T		not specified	Uncertain significance (Nov 14, 2023)
20-36591349-A-C		not specified	Uncertain significance (Mar 15, 2024)
20-36591351-A-G		not specified	Uncertain significance (Dec 28, 2023)
20-36591390-C-G		not specified	Uncertain significance (Sep 14, 2022)
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
TGIF2-RAB5IF	protein_coding	protein_coding	ENST00000558530	4	37832

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.847	0.153	125740	0	8	125748	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.857	65	87.6	0.742	0.00000493	993
Missense in Polyphen		13	22.681	0.57317		224
Synonymous	0.495	34	37.9	0.898	0.00000226	304
Loss of Function	2.72	1	10.5	0.0949	6.32e-7	104

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)	0.0000176	0.0000176
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.252
• ghis: 0.415