DUXA

double homeobox A, the group of PRD class homeoboxes and pseudogenes

Basic information

Region (hg38): 19:57154021-57167485

Links

ENSG00000258873 ∙ NCBI:503835 ∙ OMIM:611168 ∙ HGNC:32179 ∙ Uniprot:A6NLW8 ∙ 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 DUXA gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DUXA 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			14	1		15
nonsense						0
start loss						0
frameshift					1	1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	1	1

Variants in DUXA

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

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

Position	Type	Phenotype	Significance	ClinVar
19-57154428-C-T		not specified	Uncertain significance (Nov 08, 2024)
19-57154453-AG-A			Benign (Dec 31, 2019)
19-57154468-G-C		not specified	Uncertain significance (Jan 04, 2024)
19-57155314-G-A		not specified	Uncertain significance (Aug 02, 2023)
19-57158351-C-T		not specified	Uncertain significance (Sep 12, 2023)
19-57158417-T-C		not specified	Uncertain significance (Aug 27, 2024)
19-57158423-T-G		not specified	Uncertain significance (Jul 14, 2021)
19-57158453-G-A		not specified	Uncertain significance (Feb 05, 2024)
19-57158458-C-T		not specified	Uncertain significance (Jul 21, 2024)
19-57158459-G-A		not specified	Uncertain significance (Feb 16, 2023)
19-57159242-G-T		not specified	Uncertain significance (Mar 27, 2023)
19-57159248-C-T		not specified	Likely benign (Mar 31, 2023)
19-57159257-C-G		not specified	Uncertain significance (Apr 18, 2023)
19-57160644-T-G		not specified	Uncertain significance (Aug 17, 2022)
19-57160684-T-G		not specified	Uncertain significance (Nov 09, 2024)
19-57160747-G-C		not specified	Uncertain significance (Oct 12, 2024)
19-57160767-C-T		not specified	Uncertain significance (Dec 07, 2021)
19-57160774-G-A		not specified	Uncertain significance (Mar 25, 2024)
19-57160776-C-G		not specified	Uncertain significance (Nov 09, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DUXA	protein_coding	protein_coding	ENST00000554048	6	13423

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.05e-8	0.177	125728	0	20	125748	0.0000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0216	113	112	1.01	0.00000601	1336
Missense in Polyphen		29	29.914	0.96945		370
Synonymous	-0.197	40	38.4	1.04	0.00000213	366
Loss of Function	0.211	12	12.8	0.936	6.73e-7	144

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000578	0.0000578
Ashkenazi Jewish	0.00	0.00
East Asian	0.000217	0.000217
Finnish	0.000139	0.000139
European (Non-Finnish)	0.0000792	0.0000791
Middle Eastern	0.000217	0.000217
South Asian	0.0000654	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Putative transcription factor. {ECO:0000250}.

Recessive Scores

• pRec: 0.0879

Intolerance Scores

• loftool: 0.528
• rvis_EVS: 0.24
• rvis_percentile_EVS: 68.98

Haploinsufficiency Scores

• pHI: 0.113
• 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: 0.223

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;DNA binding