SPANXN2

SPANX family member N2, the group of SPANX family

Basic information

Region (hg38): X:143711954-143720752

Links

ENSG00000268988 ∙ NCBI:494119 ∙ OMIM:300665 ∙ HGNC:33175 ∙ Uniprot:Q5MJ10 ∙ 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 SPANXN2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPANXN2 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				3		3
missense			9			9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	3	0

Variants in SPANXN2

This is a list of pathogenic ClinVar variants found in the SPANXN2 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-143712077-T-C			Likely benign (Aug 01, 2022)
X-143712105-T-G		not specified	Uncertain significance (Oct 16, 2023)
X-143712109-G-C		not specified	Uncertain significance (Aug 17, 2021)
X-143712109-G-T		not specified	Uncertain significance (Aug 13, 2021)
X-143712112-G-T		not specified	Uncertain significance (Aug 12, 2021)
X-143712117-A-G		not specified	Uncertain significance (Jan 31, 2023)
X-143712124-C-T		not specified	Uncertain significance (Nov 30, 2022)
X-143712155-C-T			Likely benign (Jul 01, 2023)
X-143712202-C-T		not specified	Uncertain significance (Mar 26, 2024)
X-143712203-G-A			Likely benign (Jun 01, 2024)
X-143712241-C-T		not specified	Uncertain significance (Sep 17, 2021)
X-143712328-C-G		not specified	Uncertain significance (Jun 19, 2024)
X-143712355-C-T		not specified	Uncertain significance (May 12, 2024)
X-143712396-G-A		not specified	Uncertain significance (Aug 08, 2022)
X-143712465-T-C		not specified	Uncertain significance (Jan 05, 2022)
X-143720610-T-A		not specified	Uncertain significance (May 24, 2024)

GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0662

Intolerance Scores

• loftool: 0.812
• rvis_EVS: 0.41
• rvis_percentile_EVS: 76.67

Haploinsufficiency Scores

• pHI: 0.0211
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0829

Gene Damage Prediction

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