ITFG1

integrin alpha FG-GAP repeat containing 1

Basic information

Region (hg38): 16:47154387-47464149

Links

ENSG00000129636 ∙ NCBI:81533 ∙ OMIM:611803 ∙ HGNC:30697 ∙ Uniprot:Q8TB96 ∙ 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 ITFG1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ITFG1 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			34	1		35
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	34	1	0

Variants in ITFG1

This is a list of pathogenic ClinVar variants found in the ITFG1 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-47155748-C-A		not specified	Uncertain significance (Jan 23, 2024)
16-47158926-C-T		not specified	Uncertain significance (Aug 13, 2021)
16-47161754-G-C		not specified	Uncertain significance (May 24, 2024)
16-47161762-T-C		not specified	Uncertain significance (Sep 22, 2022)
16-47161825-C-T		not specified	Uncertain significance (Mar 11, 2024)
16-47161828-A-G		not specified	Uncertain significance (Jun 27, 2022)
16-47162550-G-T		not specified	Uncertain significance (Jun 27, 2023)
16-47162556-C-T		not specified	Uncertain significance (May 12, 2024)
16-47218937-C-T		not specified	Uncertain significance (May 08, 2024)
16-47237972-T-A		not specified	Uncertain significance (Jun 06, 2023)
16-47260633-C-A		not specified	Uncertain significance (Feb 03, 2022)
16-47260633-C-T		not specified	Likely benign (Jan 17, 2024)
16-47260634-G-A		not specified	Uncertain significance (Nov 17, 2022)
16-47260634-G-T		not specified	Uncertain significance (Jan 23, 2024)
16-47260636-G-A		not specified	Uncertain significance (Sep 01, 2021)
16-47260657-T-C		not specified	Uncertain significance (Nov 17, 2022)
16-47311260-T-C		not specified	Uncertain significance (Jan 17, 2023)
16-47311282-C-T		not specified	Uncertain significance (Aug 16, 2022)
16-47311351-A-G		not specified	Uncertain significance (Sep 17, 2021)
16-47311379-C-T		not specified	Uncertain significance (Jul 14, 2023)
16-47311381-T-C		not specified	Uncertain significance (Dec 18, 2023)
16-47311402-A-G		not specified	Uncertain significance (May 27, 2022)
16-47313735-C-T		not specified	Uncertain significance (Feb 28, 2023)
16-47313737-T-C		not specified	Uncertain significance (May 09, 2024)
16-47313749-C-G		not specified	Uncertain significance (Jul 13, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ITFG1	protein_coding	protein_coding	ENST00000320640	18	309763

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0712	0.929	125733	0	15	125748	0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.63	244	327	0.746	0.0000161	4029
Missense in Polyphen		111	149.32	0.74337		1887
Synonymous	-0.581	127	119	1.07	0.00000599	1151
Loss of Function	4.01	9	34.4	0.262	0.00000169	404

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.000191	0.000185
European (Non-Finnish)	0.0000719	0.0000703
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.000352	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Modulator of T-cell function. Has a protective effect in graft versus host disease model (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.107

Intolerance Scores

• loftool: 0.279
• rvis_EVS: -0.36
• rvis_percentile_EVS: 28.93

Haploinsufficiency Scores

• pHI: 0.279
• hipred: Y
• hipred_score: 0.625
• ghis: 0.631

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.436

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Itfg1

Gene ontology

• Cellular component: integral component of membrane;extracellular exosome