VCX3A

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

Basic information

Region (hg38): X:6533618-6535118

Previous symbols: [ "VCX3" ]

Links

ENSG00000169059 ∙ NCBI:51481 ∙ OMIM:300533 ∙ HGNC:18159 ∙ Uniprot:Q9NNX9 ∙ 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 VCX3A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the VCX3A 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				8		8
missense			43	5	3	51
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				3		3
Total	0	0	43	16	3

Variants in VCX3A

This is a list of pathogenic ClinVar variants found in the VCX3A 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-6533736-G-C		VCX3A-related disorder	Likely benign (May 18, 2023)
X-6533737-C-T		VCX3A-related disorder	Likely benign (Apr 10, 2023)
X-6533743-G-A		VCX3A-related disorder	Likely benign (May 30, 2023)
X-6533768-T-C			Likely benign (Aug 01, 2023)
X-6533772-G-C		not specified	Uncertain significance (Nov 18, 2022)
X-6533781-A-C		not specified	Uncertain significance (Nov 06, 2023)
X-6533785-A-G		not specified	Uncertain significance (Mar 01, 2024)
X-6533794-T-A		not specified	Uncertain significance (Apr 15, 2024)
X-6533795-C-T		not specified	Uncertain significance (Jul 14, 2021)
X-6533800-T-A		not specified	Uncertain significance (May 26, 2024)
X-6533800-T-C		not specified	Uncertain significance (May 31, 2023)
X-6533801-G-C		not specified	Likely benign (-)
X-6533802-G-T		not specified	Uncertain significance (Nov 27, 2023)
X-6533803-C-T		not specified	Uncertain significance (Jun 29, 2023)
X-6533804-T-C		not specified	Uncertain significance (Jan 10, 2023)
X-6533809-T-C		not specified	Uncertain significance (Jul 11, 2022)
X-6533813-T-A		not specified	Uncertain significance (Jan 19, 2022)
X-6533813-T-C		not specified	Uncertain significance (Aug 02, 2023)
X-6533821-T-C		not specified	Uncertain significance (Sep 14, 2023)
X-6533823-C-A		not specified	Uncertain significance (Sep 27, 2021)
X-6533828-C-T		not specified	Benign (Nov 19, 2015)
X-6533832-G-A			Likely benign (Jan 01, 2024)
X-6533833-C-G		not specified	Uncertain significance (Feb 15, 2023)
X-6533840-G-T		not specified	Uncertain significance (May 20, 2024)
X-6533845-A-G		not specified	Likely benign (Jul 21, 2015)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
VCX3A	protein_coding	protein_coding	ENST00000381089	2	1501

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.310	0.500	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-2.14	86	45.4	1.89	0.00000365	1138
Missense in Polyphen
Synonymous	-3.02	42	23.4	1.79	0.00000242	333
Loss of Function	0.479	0	0.268	0.00	1.68e-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: 0.0607
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0500

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
• Cellular component: nucleus;nucleolus