VCX2

variable charge X-linked 2, the group of Variable charge X/Y family

Basic information

Region (hg38): X:8169944-8171267

Links

ENSG00000177504 ∙ NCBI:51480 ∙ OMIM:300532 ∙ HGNC:18158 ∙ Uniprot:Q9H322 ∙ 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 VCX2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the VCX2 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				6		6
missense			37	3	1	41
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	37	9	1

Variants in VCX2

This is a list of pathogenic ClinVar variants found in the VCX2 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-8170037-C-G		not specified	Uncertain significance (Apr 26, 2023)
X-8170042-C-T		not specified	Uncertain significance (Mar 25, 2024)
X-8170052-C-G		not specified	Uncertain significance (Mar 21, 2022)
X-8170052-C-T		not specified	Likely benign (Nov 09, 2021)
X-8170056-G-A			Likely benign (Jul 01, 2022)
X-8170060-A-T		not specified	Likely benign (Oct 05, 2023)
X-8170078-G-A		not specified	Uncertain significance (Sep 26, 2023)
X-8170078-G-C		not specified	Uncertain significance (Dec 16, 2023)
X-8170102-T-C		not specified	Uncertain significance (Jan 03, 2022)
X-8170107-A-T		not specified	Uncertain significance (May 15, 2024)
X-8170109-T-G		not specified	Uncertain significance (Mar 23, 2022)
X-8170119-T-C			Likely benign (Mar 30, 2018)
X-8170129-C-G			Benign (Mar 30, 2018)
X-8170143-G-T			Likely benign (Oct 01, 2022)
X-8170145-G-T		not specified	Uncertain significance (Feb 15, 2023)
X-8170149-G-C		not specified	Uncertain significance (Jun 24, 2022)
X-8170151-G-C		not specified	Uncertain significance (Jun 24, 2022)
X-8170156-G-C		not specified	Likely benign (Jun 24, 2022)
X-8170159-C-T		not specified	Uncertain significance (Jun 24, 2022)
X-8170163-C-T		not specified	Uncertain significance (Aug 13, 2021)
X-8170164-G-C		not specified	Uncertain significance (Jul 26, 2022)
X-8170178-C-T		not specified	Uncertain significance (Mar 13, 2023)
X-8170179-C-T			Likely benign (Apr 01, 2022)
X-8170180-G-A		not specified	Uncertain significance (Jan 09, 2024)
X-8170181-G-A			Likely benign (-)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
VCX2	protein_coding	protein_coding	ENST00000317103	2	1320

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0581	0.506	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-4.99	142	46.3	3.07	0.00000431	860
Missense in Polyphen
Synonymous	-5.72	59	23.6	2.50	0.00000268	266
Loss of Function	-1.82	1	0.176	5.68	1.11e-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.

Recessive Scores

• pRec: 0.0940

Haploinsufficiency Scores

• pHI: 0.0752
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0522

Gene Damage Prediction

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

Gene ontology

• Biological process: brain development;biological_process
• Cellular component: cellular_component
• Molecular function: molecular_function