VCX3B

variable charge X-linked 3B, the group of Variable charge X/Y family

Basic information

Region (hg38): X:8464830-8466510

Links

ENSG00000205642 ∙ ∙ OMIM:300981 ∙ HGNC:31838 ∙ Uniprot:Q9H321 ∙ 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 VCX3B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the VCX3B 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				12		12
missense			49	7		56
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	49	20	0

Variants in VCX3B

This is a list of pathogenic ClinVar variants found in the VCX3B 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-8465457-C-T		not specified	Conflicting classifications of pathogenicity (Nov 01, 2022)
X-8465527-C-T		not specified	Likely benign (Dec 01, 2022)
X-8465746-C-A		not specified	Uncertain significance (Oct 26, 2022)
X-8465760-A-G		not specified	Uncertain significance (Sep 28, 2021)
X-8465769-A-G		not specified	Uncertain significance (Sep 29, 2022)
X-8465781-A-G		not specified	Likely benign (Apr 08, 2024)
X-8465809-C-G		not specified	Uncertain significance (Jan 26, 2022)
X-8465809-C-T		not specified	Uncertain significance (Oct 06, 2021)
X-8465821-C-A		not specified	Uncertain significance (Jun 18, 2024)
X-8465826-G-A		not specified	Uncertain significance (Jan 27, 2022)
X-8465830-C-T		not specified	Uncertain significance (Feb 27, 2024)
X-8465851-G-T		not specified	Uncertain significance (Apr 28, 2022)
X-8465853-C-T		not specified	Uncertain significance (Dec 28, 2022)
X-8465868-C-T		not specified	Uncertain significance (Feb 22, 2023)
X-8465889-G-A		not specified	Uncertain significance (Jun 07, 2024)
X-8465892-C-T		not specified	Uncertain significance (Dec 16, 2023)
X-8465911-C-T		not specified	Uncertain significance (Dec 20, 2023)
X-8465912-G-A			Likely benign (Jul 01, 2022)
X-8465913-C-T		not specified	Uncertain significance (Nov 18, 2022)
X-8465914-C-T		not specified	Uncertain significance (Jan 09, 2024)
X-8465916-G-A		not specified	Uncertain significance (Apr 25, 2022)
X-8465919-G-A		not specified	Uncertain significance (Sep 06, 2022)
X-8465929-G-C		not specified	Uncertain significance (May 02, 2024)
X-8465931-G-C		not specified	Uncertain significance (Jul 26, 2022)
X-8465946-G-A		not specified	Uncertain significance (May 07, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
VCX3B	protein_coding	protein_coding	ENST00000381032	2	1680

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.337	0.497	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.64	102	64.9	1.57	0.00000513	1560
Missense in Polyphen
Synonymous	-1.61	41	29.8	1.38	0.00000286	423
Loss of Function	0.662	0	0.510	0.00	3.20e-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.

Haploinsufficiency Scores

• pHI: 0.0437
• hipred: N
• hipred_score: 0.187

Essentials

• essential_gene_CRISPR: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00683

Gene Damage Prediction

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

Gene ontology

• Biological process: brain development
• Cellular component: nucleus;nucleolus