HDX

highly divergent homeobox, the group of POU class homeoboxes and pseudogenes

Basic information

Region (hg38): X:84317874-84502479

Previous symbols: [ "CXorf43" ]

Links

ENSG00000165259 ∙ NCBI:139324 ∙ OMIM:300994 ∙ HGNC:26411 ∙ Uniprot:Q7Z353 ∙ 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 HDX gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HDX 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					5	5
missense			20	1	1	22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	1	6

Variants in HDX

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

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

Position	Type	Phenotype	Significance	ClinVar
X-84321930-C-A		not specified	Uncertain significance (Dec 20, 2021)
X-84321944-T-A		not specified	Uncertain significance (Sep 14, 2023)
X-84321977-A-T			Uncertain significance (Jul 01, 2024)
X-84322014-C-T		not specified	Uncertain significance (Apr 29, 2024)
X-84326256-C-T			Benign (Jul 16, 2018)
X-84333786-T-A		not specified	Uncertain significance (Feb 02, 2024)
X-84333840-T-G		not specified	Uncertain significance (Dec 19, 2023)
X-84344255-G-A		not specified	Uncertain significance (Jul 05, 2022)
X-84361503-A-G		not specified	Uncertain significance (May 06, 2022)
X-84361532-G-A			Benign (Jul 16, 2018)
X-84361554-T-C		not specified	Uncertain significance (Apr 18, 2023)
X-84361584-C-T		not specified	Likely benign (Oct 27, 2022)
X-84440548-C-A		not specified	Uncertain significance (May 08, 2024)
X-84440551-C-G		not specified	Uncertain significance (Oct 05, 2023)
X-84440567-C-G		not specified	Uncertain significance (Jul 20, 2022)
X-84468543-G-A		not specified	Uncertain significance (Jan 02, 2024)
X-84468603-T-C		not specified	Uncertain significance (Apr 22, 2022)
X-84468830-A-G		not specified	Uncertain significance (Mar 24, 2023)
X-84468904-G-A			Benign (Jul 23, 2018)
X-84469012-G-A			Benign (Apr 16, 2018)
X-84469029-T-C		not specified	Uncertain significance (May 09, 2023)
X-84469119-C-T		not specified	Uncertain significance (Sep 29, 2023)
X-84469146-C-T			Benign (Apr 16, 2018)
X-84469203-T-C		not specified	Uncertain significance (May 31, 2023)
X-84469335-T-C		not specified	Uncertain significance (Aug 19, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HDX	protein_coding	protein_coding	ENST00000297977	9	184606

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0759	0.924	125673	3	11	125687	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.129	227	233	0.976	0.0000164	4518
Missense in Polyphen		58	78.841	0.73566		1518
Synonymous	0.0435	81	81.5	0.994	0.00000560	1291
Loss of Function	3.08	6	21.3	0.281	0.00000163	400

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000343	0.000326
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000129	0.0000924
European (Non-Finnish)	0.0000628	0.0000440
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.104

Intolerance Scores

• loftool: 0.419
• rvis_EVS: -0.03
• rvis_percentile_EVS: 51.92

Haploinsufficiency Scores

• pHI: 0.391
• hipred: Y
• hipred_score: 0.547
• ghis: 0.492

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.774

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hdx
• Phenotype: normal phenotype

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