SPATS2

spermatogenesis associated serine rich 2

Basic information

Region (hg38): 12:49366584-49527425

Links

ENSG00000123352 ∙ NCBI:65244 ∙ OMIM:611667 ∙ HGNC:18650 ∙ Uniprot:Q86XZ4 ∙ 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 SPATS2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPATS2 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			40	2	1	43
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	40	2	1

Variants in SPATS2

This is a list of pathogenic ClinVar variants found in the SPATS2 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-49484607-T-G		not specified	Uncertain significance (Mar 02, 2023)
12-49484625-A-G		not specified	Uncertain significance (Feb 28, 2023)
12-49484628-G-A			Benign (Jan 19, 2018)
12-49484638-A-G		not specified	Uncertain significance (May 17, 2023)
12-49489472-C-T		not specified	Uncertain significance (Apr 19, 2023)
12-49489474-G-A		not specified	Uncertain significance (Aug 26, 2022)
12-49489499-G-A		not specified	Uncertain significance (Apr 26, 2024)
12-49494763-C-T		not specified	Uncertain significance (Dec 03, 2021)
12-49494774-G-A		not specified	Uncertain significance (May 10, 2024)
12-49494790-G-A		not specified	Uncertain significance (Jul 22, 2024)
12-49494891-A-G		not specified	Uncertain significance (Aug 05, 2024)
12-49494892-A-G		not specified	Uncertain significance (Mar 20, 2023)
12-49494928-T-G		not specified	Uncertain significance (Sep 14, 2023)
12-49494988-C-T		not specified	Likely benign (Mar 28, 2024)
12-49496846-G-C		not specified	Uncertain significance (Jun 24, 2022)
12-49496911-C-G		not specified	Uncertain significance (Jan 09, 2024)
12-49496980-A-C		not specified	Uncertain significance (Sep 15, 2021)
12-49500087-T-C		not specified	Uncertain significance (Sep 23, 2023)
12-49500123-G-A		not specified	Uncertain significance (Dec 08, 2023)
12-49500133-G-A		not specified	Uncertain significance (Nov 11, 2024)
12-49500138-G-T		not specified	Uncertain significance (Oct 07, 2024)
12-49500147-G-C		not specified	Uncertain significance (Aug 14, 2024)
12-49500153-A-G		not specified	Uncertain significance (Jun 22, 2023)
12-49500154-T-C		not specified	Uncertain significance (Jun 05, 2023)
12-49514575-C-T		not specified	Uncertain significance (Nov 16, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPATS2	protein_coding	protein_coding	ENST00000553127	12	160839

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.972	0.0276	125174	2	572	125748	0.00229

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.796	258	297	0.870	0.0000156	3583
Missense in Polyphen		85	111.97	0.75917		1368
Synonymous	0.636	99	107	0.922	0.00000586	1047
Loss of Function	4.27	4	28.7	0.139	0.00000172	333

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000329	0.000329
Ashkenazi Jewish	0.00188	0.00189
East Asian	0.0000544	0.0000544
Finnish	0.0112	0.0112
European (Non-Finnish)	0.00242	0.00241
Middle Eastern	0.0000544	0.0000544
South Asian	0.000490	0.000490
Other	0.00244	0.00245

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0849

Intolerance Scores

• loftool: 0.132
• rvis_EVS: -0.27
• rvis_percentile_EVS: 34.71

Haploinsufficiency Scores

• pHI: 0.119
• hipred: N
• hipred_score: 0.376
• ghis: 0.574

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.182

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Spats2

Gene ontology

• Cellular component: cytoplasm;cytosol
• Molecular function: RNA binding