IFRD1

interferon related developmental regulator 1, the group of Armadillo like helical domain containing

Basic information

Region (hg38): 7:112422886-112481017

Links

ENSG00000006652 ∙ NCBI:3475 ∙ OMIM:603502 ∙ HGNC:5456 ∙ Uniprot:O00458 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• spinocerebellar ataxia type 18 (Supportive), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the IFRD1 gene.

• Inborn genetic diseases (17 variants)
• not provided (6 variants)
• not specified (2 variants)
• Charcot-Marie-Tooth disease (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IFRD1 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					3	3
missense			17	1	1	19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	17	1	4

Variants in IFRD1

This is a list of pathogenic ClinVar variants found in the IFRD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-112450695-A-C		not specified	Uncertain significance (Jul 10, 2023)
7-112450727-T-C			Benign (Mar 30, 2018)
7-112450761-G-A		not specified	Uncertain significance (Jun 17, 2022)
7-112455810-A-G		not specified	Uncertain significance (May 25, 2022)
7-112455859-C-G		not specified	Uncertain significance (Apr 25, 2023)
7-112455988-A-C		not specified	Benign (-)
7-112456015-T-A		not specified	Benign (Jul 01, 2023)
7-112456018-T-C		not specified	Benign (-)
7-112456914-T-C		not specified	Likely benign (Oct 13, 2023)
7-112457000-T-C		not specified	Uncertain significance (Jan 16, 2024)
7-112458879-G-A		not specified	Uncertain significance (Dec 28, 2023)
7-112458965-A-G		Charcot-Marie-Tooth disease • IFRD1-related disorder	Likely benign (May 22, 2023)
7-112461852-ATT-A		not specified	Benign (-)
7-112461852-A-AT		IFRD1-related disorder	Likely benign (Mar 07, 2023)
7-112461854-T-A		not specified	Benign (-)
7-112461856-T-A		not specified	Benign/Likely benign (-)
7-112461996-A-G			Benign (Dec 31, 2019)
7-112462016-C-G		not specified	Benign (Dec 31, 2019)
7-112462034-A-G		not specified	Uncertain significance (Dec 14, 2023)
7-112462104-A-C		not specified	Uncertain significance (Apr 07, 2022)
7-112462112-T-A		not specified	Uncertain significance (Jan 29, 2024)
7-112462113-C-A		not specified	Uncertain significance (Jan 29, 2024)
7-112462300-T-G		not specified	Benign (-)
7-112462357-A-T		not specified	Uncertain significance (Jun 29, 2023)
7-112462373-G-A		not specified	Uncertain significance (Jun 13, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IFRD1	protein_coding	protein_coding	ENST00000403825	12	58050

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00121	0.997	125727	0	21	125748	0.0000835

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.26	191	247	0.774	0.0000129	2967
Missense in Polyphen		61	83.014	0.73481		1124
Synonymous	0.539	79	85.3	0.926	0.00000426	850
Loss of Function	2.74	9	23.3	0.386	0.00000119	301

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000116	0.000116
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.0000889	0.0000879
Middle Eastern	0.000163	0.000163
South Asian	0.0000327	0.0000327
Other	0.000494	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Could play a role in regulating gene activity in the proliferative and/or differentiative pathways induced by NGF. May be an autocrine factor that attenuates or amplifies the initial ligand-induced signal (By similarity). {ECO:0000250}.
• Pathway: miR-targeted genes in epithelium - TarBase;miR-targeted genes in leukocytes - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;Hypertrophy Model (Consensus)

Recessive Scores

• pRec: 0.125

Intolerance Scores

• loftool: 0.490
• rvis_EVS: -0.38
• rvis_percentile_EVS: 27.69

Haploinsufficiency Scores

• pHI: 0.625
• hipred: Y
• hipred_score: 0.704
• ghis: 0.467

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.967

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ifrd1
• Phenotype: growth/size/body region phenotype; muscle phenotype

Gene ontology

• Biological process: myoblast fate determination;striated muscle tissue development;negative regulation of axon extension;muscle cell differentiation;skeletal muscle tissue regeneration;negative regulation of collateral sprouting
• Cellular component: nucleus;cytoplasm