SPANXC

protein-coding

SPANX family member C, the group of SPANX family

Gene summary

Temporally regulated transcription and translation of several testis-specific genes is required to initiate the series of molecular and morphological changes in the male germ cell lineage necessary for the formation of mature spermatozoa. This gene is a member of the SPANX family, which is located in a gene cluster on chromosome X. The SPANX genes encode differentially expressed testis-specific proteins that localize to various subcellular compartments. This particular gene encodes a protein that localizes to the nucleus and is expressed in highly metastatic cell lines, making the protein a potential diagnostic and prognostic marker. The protein belongs to a family of cancer/testis antigens and represents a potential target for cancer immunotherapy. [provided by RefSeq, Jul 2008]

MANE transcript

NM_022661.4

Inheritance

—

ClinVar variants

B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.75

Max pathogenic AF

—

Genomic locus

chrX:141,241,463-141,242,517

External References & Databases

Ensembl (ENSG00000198573)

Transcript & Mutation Effects

hg38 • Region Span ~1.1 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 SPANXC variants in ClinVar

1 Conditions Cataloged

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_022661.4. 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						0
missense				2 clinvar		2
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	0	2	0	2

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 2 of 2 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_022661.4	RefSeq	NP_073152.2	2	MANE Select
ENST00000358993.3	Ensembl	ENSP00000351884.2	2	MANE Select

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

biological_process

Molecular Function

molecular_function
protein binding

Cellular Component

nucleus
cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000358993
Coding exons: 2
Length: 1034
Individuals with no LoFs: 101335
Homozygous LoFs: 1
Heterozygous LoFs: 0
Defined: 101336
p: 0.00000493

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-2.49	77	35.4	2.18	0.00000276	604
Missense (PolyPhen)		28	14.513	1.9293		269
Synonymous	-1.37	23	16.0	1.43	0.00000161	172
Loss of Function	-0.524	1	0.572	1.75	3.63e-8	11

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	0.000078	0.000060	rare
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

Intolerance Scores

LoFtool: 0.904
RVIS EVS: 1.53
RVIS percentile EVS: 95.48

Essentials

Essential (CRISPR): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0440

Gene Damage Prediction

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