SPANXN4

SPANX family member N4, the group of SPANX family

Basic information

Region (hg38): X:143025927-143034702

Links

ENSG00000189326 ∙ NCBI:441525 ∙ OMIM:300667 ∙ HGNC:33177 ∙ Uniprot:Q5MJ08 ∙ 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 SPANXN4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPANXN4 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						0
missense			8	2		10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	2	0

Variants in SPANXN4

This is a list of pathogenic ClinVar variants found in the SPANXN4 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-143026043-A-G		not specified	Likely benign (Jan 17, 2024)
X-143034034-A-C		not specified	Likely benign (Feb 16, 2023)
X-143034037-C-A		not specified	Uncertain significance (May 16, 2022)
X-143034038-T-C		not specified	Uncertain significance (Jan 24, 2024)
X-143034046-G-A		not specified	Uncertain significance (Jan 06, 2023)
X-143034063-G-C		not specified	Uncertain significance (Mar 21, 2023)
X-143034066-T-A		not specified	Uncertain significance (May 31, 2022)
X-143034115-A-G			Uncertain significance (-)
X-143034159-G-T		not specified	Uncertain significance (Jan 05, 2022)
X-143034160-C-G		not specified	Uncertain significance (Feb 07, 2023)
X-143034233-G-A		not specified	Uncertain significance (Mar 30, 2024)
X-143034239-A-G		not specified	Uncertain significance (Oct 25, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPANXN4	protein_coding	protein_coding	ENST00000446864	2	8785

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.352	0.494	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.30	47	27.7	1.69	0.00000180	642
Missense in Polyphen		8	2.3412	3.4171		55
Synonymous	0.169	10	10.7	0.934	7.58e-7	169
Loss of Function	0.745	0	0.646	0.00	4.08e-8	14

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

Recessive Scores

• pRec: 0.0717

Intolerance Scores

• loftool: 0.744
• rvis_EVS: 0.26
• rvis_percentile_EVS: 69.83

Haploinsufficiency Scores

• pHI: 0.0166
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00993

Gene Damage Prediction

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