SPANXN5

SPANX family member N5, the group of SPANX family

Basic information

Region (hg38): X:52796144-52797427

Links

ENSG00000204363 ∙ NCBI:494197 ∙ OMIM:300668 ∙ HGNC:33178 ∙ Uniprot:Q5MJ07 ∙ 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 SPANXN5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPANXN5 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			5			5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	5	0	0

Variants in SPANXN5

This is a list of pathogenic ClinVar variants found in the SPANXN5 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-52796495-T-G		not specified	Uncertain significance (Apr 18, 2023)
X-52796511-G-T		not specified	Uncertain significance (Dec 15, 2024)
X-52796537-C-T		not specified	Uncertain significance (Aug 13, 2021)
X-52796565-A-T		not specified	Uncertain significance (Feb 27, 2024)
X-52796606-A-G		not specified	Uncertain significance (Sep 26, 2023)
X-52796616-T-C		not specified	Uncertain significance (May 31, 2023)
X-52797326-G-C		not specified	Uncertain significance (Feb 12, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPANXN5	protein_coding	protein_coding	ENST00000375511	2	1958

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0852	0.573	125690	1	0	125691	0.00000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.179	27	24.5	1.10	0.00000167	476
Missense in Polyphen		6	7.176	0.83612		161
Synonymous	0.0435	10	10.2	0.983	7.64e-7	119
Loss of Function	-0.135	1	0.865	1.16	5.44e-8	16

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)	0.0000122	0.00000880
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: -0.03
• rvis_percentile_EVS: 51.04

Haploinsufficiency Scores

• pHI: 0.000160
• hipred: N
• hipred_score: 0.112
• ghis: 0.401

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Low	Low	Low
Primary Immunodeficiency	Low	Low	Low
Cancer	Low	Low	Low