IFRD2

interferon related developmental regulator 2, the group of Armadillo like helical domain containing

Basic information

Region (hg38): 3:50287732-50292918

Links

ENSG00000214706 ∙ NCBI:7866 ∙ OMIM:602725 ∙ HGNC:5457 ∙ Uniprot:Q12894 ∙ 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 IFRD2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IFRD2 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			33	1	1	35
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			8			8
Total	0	0	41	1	1

Variants in IFRD2

This is a list of pathogenic ClinVar variants found in the IFRD2 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-50288217-G-A		not specified	Uncertain significance (Aug 18, 2023)
3-50288222-C-T		not specified	Uncertain significance (May 30, 2024)
3-50288419-C-A		not specified	Uncertain significance (Jan 26, 2023)
3-50288444-C-A		not specified	Uncertain significance (Feb 10, 2022)
3-50288483-T-C		not specified	Uncertain significance (Nov 17, 2022)
3-50288491-A-G		not specified	Uncertain significance (Jul 12, 2023)
3-50288492-G-A		not specified	Uncertain significance (Mar 19, 2024)
3-50288501-T-C		not specified	Uncertain significance (Apr 07, 2023)
3-50288605-G-A		not specified	Uncertain significance (Mar 31, 2024)
3-50288639-G-A		not specified	Uncertain significance (Aug 05, 2024)
3-50288655-G-T		not specified	Uncertain significance (May 01, 2024)
3-50288659-A-G		not specified	Uncertain significance (Mar 29, 2024)
3-50288660-T-C		not specified	Likely benign (Nov 10, 2024)
3-50288678-C-T		not specified	Uncertain significance (Feb 22, 2023)
3-50288843-C-T		not specified	Uncertain significance (Apr 07, 2023)
3-50288868-T-C		not specified	Uncertain significance (Dec 12, 2022)
3-50288891-C-T		not specified	Uncertain significance (Nov 12, 2024)
3-50288900-C-G		not specified	Uncertain significance (Dec 04, 2024)
3-50288922-C-T		not specified	Uncertain significance (May 24, 2024)
3-50288925-A-G		not specified	Uncertain significance (Jan 23, 2024)
3-50289261-G-T		not specified	Uncertain significance (Jun 06, 2023)
3-50289305-C-T		not specified	Uncertain significance (Sep 04, 2024)
3-50289310-C-T		not specified	Uncertain significance (Sep 20, 2024)
3-50289350-G-A		not specified	Uncertain significance (Jun 23, 2023)
3-50289467-T-A		not specified	Likely benign (Apr 24, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IFRD2	protein_coding	protein_coding	ENST00000429673	12	5187

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.10e-9	0.528	124888	0	26	124914	0.000104

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.153	305	313	0.976	0.0000200	3138
Missense in Polyphen		123	128.48	0.95735		1275
Synonymous	-1.24	146	128	1.14	0.00000744	1091
Loss of Function	1.17	17	23.1	0.737	0.00000108	255

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000154	0.000151
Ashkenazi Jewish	0.000100	0.0000993
East Asian	0.000111	0.000111
Finnish	0.00	0.00
European (Non-Finnish)	0.000137	0.000133
Middle Eastern	0.000111	0.000111
South Asian	0.000102	0.0000980
Other	0.000167	0.000165

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.140

Intolerance Scores

• rvis_EVS: 0.2
• rvis_percentile_EVS: 67.36

Haploinsufficiency Scores

• pHI: 0.217
• hipred: N
• hipred_score: 0.197
• ghis: 0.499

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• gene_indispensability_pred: E
• gene_indispensability_score: 0.942

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ifrd2

Gene ontology

• Cellular component: nucleus
• Molecular function: molecular_function;protein binding