VCX

variable charge X-linked, the group of Variable charge X/Y family

Basic information

Region (hg38): X:7842262-7844143

Links

ENSG00000182583 ∙ NCBI:26609 ∙ OMIM:300229 ∙ HGNC:12667 ∙ Uniprot:Q9H320 ∙ 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 VCX gene.

Variants pathogenicity by type

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

Variants in VCX

This is a list of pathogenic ClinVar variants found in the VCX 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-7843210-C-T			Likely benign (Feb 01, 2024)
X-7843611-G-A			Likely benign (Jan 01, 2023)
X-7843886-T-C			Uncertain significance (-)
X-7843943-C-T			Likely benign (-)
X-7843963-G-A			Likely benign (Jan 01, 2023)
X-7843993-A-G			Likely benign (Jul 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
VCX	protein_coding	protein_coding	ENST00000381059	2	1882

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.344	0.496	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-2.81	144	75.4	1.91	0.00000664	1274
Missense in Polyphen
Synonymous	-2.11	50	34.3	1.46	0.00000347	351
Loss of Function	0.704	0	0.577	0.00	3.62e-8	18

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May mediate a process in spermatogenesis or may play a role in sex ratio distortion.

Intolerance Scores

• loftool: 0.845
• rvis_EVS: 2.15
• rvis_percentile_EVS: 97.98

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00319

Gene Damage Prediction

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

Gene ontology

• Biological process: chromatin organization;spermatogenesis;brain development;ribosome assembly
• Cellular component: nucleus;nucleolus
• Molecular function: chromatin binding