SPATA18

spermatogenesis associated 18

Basic information

Region (hg38): 4:52051304-52097299

Links

ENSG00000163071 ∙ NCBI:132671 ∙ OMIM:612814 ∙ HGNC:29579 ∙ Uniprot:Q8TC71 ∙ 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 SPATA18 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPATA18 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			28	3	1	32
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	28	3	1

Variants in SPATA18

This is a list of pathogenic ClinVar variants found in the SPATA18 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
4-52051709-C-T		not specified	Uncertain significance (Feb 28, 2024)
4-52060419-A-G		not specified	Uncertain significance (May 29, 2024)
4-52060504-T-C		not specified	Uncertain significance (Dec 27, 2022)
4-52060788-G-A		not specified	Likely benign (May 27, 2022)
4-52060799-G-A		not specified	Uncertain significance (Nov 11, 2024)
4-52062224-C-T		not specified	Uncertain significance (Nov 12, 2021)
4-52062304-C-T		not specified	Uncertain significance (Oct 26, 2022)
4-52062305-G-A		not specified	Uncertain significance (Apr 17, 2023)
4-52062330-C-G		not specified	Uncertain significance (Jun 25, 2024)
4-52069865-C-T		not specified	Uncertain significance (Jul 06, 2021)
4-52071939-G-A		not specified	Uncertain significance (Sep 10, 2024)
4-52071948-C-G		not specified	Uncertain significance (Jan 23, 2023)
4-52072044-C-G		not specified	Uncertain significance (Sep 16, 2021)
4-52072099-G-A			Likely benign (Mar 06, 2018)
4-52072119-G-T		not specified	Uncertain significance (Nov 21, 2023)
4-52076789-A-T		not specified	Uncertain significance (Jul 27, 2024)
4-52076798-C-T		not specified	Uncertain significance (Oct 07, 2024)
4-52076813-C-T		not specified	Uncertain significance (Nov 26, 2024)
4-52076820-G-A			Likely benign (Mar 28, 2018)
4-52076835-G-A		not specified	Uncertain significance (Feb 13, 2023)
4-52076885-A-G		not specified	Uncertain significance (Jan 03, 2024)
4-52076888-C-A		not specified	Uncertain significance (Sep 16, 2021)
4-52076895-A-G			Benign (Mar 28, 2018)
4-52076910-C-T		not specified	Uncertain significance (Apr 26, 2024)
4-52076988-G-A		not specified	Uncertain significance (Jan 23, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPATA18	protein_coding	protein_coding	ENST00000295213	13	45962

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.01e-13	0.262	125652	0	96	125748	0.000382

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.409	331	311	1.07	0.0000168	3523
Missense in Polyphen		138	144.26	0.95661		1663
Synonymous	-0.892	125	113	1.11	0.00000579	1036
Loss of Function	1.16	24	30.9	0.775	0.00000165	346

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00141	0.00141
Ashkenazi Jewish	0.000298	0.000298
East Asian	0.000327	0.000326
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000229	0.000229
Middle Eastern	0.000327	0.000326
South Asian	0.000807	0.000784
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Key regulator of mitochondrial quality that mediates the repairing or degradation of unhealthy mitochondria in response to mitochondrial damage. Mediator of mitochondrial protein catabolic process (also named MALM) by mediating the degradation of damaged proteins inside mitochondria by promoting the accumulation in the mitochondrial matrix of hydrolases that are characteristic of the lysosomal lumen. Also involved in mitochondrion degradation of damaged mitochondria by promoting the formation of vacuole-like structures (named MIV), which engulf and degrade unhealthy mitochondria by accumulating lysosomes. The physical interaction of SPATA18/MIEAP, BNIP3 and BNIP3L/NIX at the mitochondrial outer membrane regulates the opening of a pore in the mitochondrial double membrane in order to mediate the translocation of lysosomal proteins from the cytoplasm to the mitochondrial matrix. {ECO:0000269|PubMed:21264221, ECO:0000269|PubMed:21264228, ECO:0000269|PubMed:22292033}.
• Pathway: Validated transcriptional targets of TAp63 isoforms (Consensus)

Recessive Scores

• pRec: 0.0795

Intolerance Scores

• loftool: 0.511
• rvis_EVS: 0.11
• rvis_percentile_EVS: 62.14

Haploinsufficiency Scores

• pHI: 0.190
• hipred: N
• hipred_score: 0.177
• ghis: 0.428

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0371

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Spata18
• Phenotype: cellular phenotype; digestive/alimentary phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hematopoietic system phenotype; neoplasm

Gene ontology

• Biological process: cellular response to DNA damage stimulus;mitochondrial protein catabolic process;mitophagy by induced vacuole formation
• Cellular component: cytoplasm;mitochondrial outer membrane;intracellular membrane-bounded organelle
• Molecular function: protein binding