VCX2

protein-coding

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

Gene summary

This gene belongs to the VCX/Y gene family, which has multiple members on both X and Y chromosomes that are expressed exclusively in male germ cells. The VCX gene cluster is polymorphic in terms of copy number; different individuals may have a different number of VCX genes. This gene contains two copies of a 30 nt tandem repeat. Deletion of a nearby member of this family was implicated in cognitive disability. [provided by RefSeq, Feb 2015]

MANE transcript

NM_016378.3

Inheritance

—

ClinVar variants

U:67B:9

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 5.68

Max pathogenic AF

—

Genomic locus

chrX:8,169,944-8,171,267

External References & Databases

Ensembl (ENSG00000177504)

Transcript & Mutation Effects

hg38 • Region Span ~1.3 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to VCX2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 70

not providedTotal: 6

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_016378.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				5 clinvar		5
missense			67 clinvar	4 clinvar		71
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	67	9	0	76

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 3 of 3 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_016378.3	RefSeq	NP_057462.2	2	MANE Select
ENST00000317103.5	Ensembl	ENSP00000321309.4	2	MANE Select
ENST00001098329.1	Ensembl	ENSP00000768135.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

brain development
biological_process

Molecular Function

molecular_function

Cellular Component

cellular_component

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000317103
Coding exons: 2
Length: 1320
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-4.99	142	46.3	3.07	0.00000431	860
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

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

Recessive Scores

pRec: 0.0940

Essentials

Essential (CRISPR): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0522

Gene Damage Prediction

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