ARGFX

arginine-fifty homeobox, the group of PRD class homeoboxes and pseudogenes

Basic information

Region (hg38): 3:121567949-121590622

Links

ENSG00000186103 ∙ NCBI:503582 ∙ OMIM:611164 ∙ HGNC:30146 ∙ Uniprot:A6NJG6 ∙ 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 ARGFX gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARGFX 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			16	4		20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	4	0

Variants in ARGFX

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

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

Position	Type	Phenotype	Significance	ClinVar
3-121570782-G-A		not specified	Likely benign (Apr 04, 2024)
3-121570785-G-C		not specified	Likely benign (Dec 15, 2023)
3-121570813-C-T		not specified	Uncertain significance (Jan 23, 2023)
3-121584941-G-A		not specified	Uncertain significance (Aug 10, 2021)
3-121584997-A-G		not specified	Uncertain significance (Jun 24, 2022)
3-121585021-G-C		not specified	Uncertain significance (Jun 07, 2023)
3-121585028-T-C		not specified	Uncertain significance (Nov 21, 2023)
3-121585037-G-C		not specified	Uncertain significance (Nov 14, 2023)
3-121585042-G-A		not specified	Likely benign (May 31, 2023)
3-121586037-C-T		not specified	Uncertain significance (Jan 30, 2024)
3-121586041-G-A		not specified	Uncertain significance (May 18, 2023)
3-121586055-A-C		not specified	Uncertain significance (Oct 25, 2022)
3-121586097-C-T		not specified	Uncertain significance (Mar 16, 2022)
3-121586122-C-T		not specified	Uncertain significance (Dec 26, 2023)
3-121586143-G-A		not specified	Likely benign (Jan 08, 2024)
3-121586336-C-G		not specified	Uncertain significance (Nov 30, 2022)
3-121586454-C-T		not specified	Uncertain significance (Sep 20, 2023)
3-121586469-G-A		not specified	Uncertain significance (Oct 18, 2021)
3-121586499-A-C		not specified	Uncertain significance (May 16, 2023)
3-121586524-C-G		not specified	Likely benign (Jun 28, 2022)
3-121586529-G-A		not specified	Uncertain significance (May 10, 2024)
3-121586569-C-T		not specified	Uncertain significance (Apr 08, 2024)
3-121586595-C-A		not specified	Uncertain significance (Oct 06, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ARGFX	protein_coding	protein_coding	ENST00000334384	4	15931

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000296	0.362	125686	0	13	125699	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.157	152	158	0.965	0.00000772	2049
Missense in Polyphen		14	23.411	0.598		317
Synonymous	-1.74	77	59.9	1.29	0.00000293	620
Loss of Function	-0.180	5	4.59	1.09	1.93e-7	68

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000294	0.0000294
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000570	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000449	0.0000440
Middle Eastern	0.0000570	0.0000544
South Asian	0.000229	0.000163
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Putative transcription factor. {ECO:0000250}.
• Pathway: Preimplantation Embryo (Consensus)

Recessive Scores

• pRec: 0.0522

Intolerance Scores

• loftool: 0.297
• rvis_EVS: 0.33
• rvis_percentile_EVS: 73.27

Haploinsufficiency Scores

• pHI: 0.0225
• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00253

Gene Damage Prediction

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

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;sequence-specific DNA binding