SPATS2L

spermatogenesis associated serine rich 2 like

Basic information

Region (hg38): 2:200305880-200482264

Links

ENSG00000196141 ∙ NCBI:26010 ∙ OMIM:613817 ∙ HGNC:24574 ∙ Uniprot:Q9NUQ6 ∙ 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 SPATS2L gene.

• Inborn genetic diseases (21 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPATS2L 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			21	1		22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	1	0

Variants in SPATS2L

This is a list of pathogenic ClinVar variants found in the SPATS2L region.

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

Position	Type	Phenotype	Significance	ClinVar
2-200389254-C-G		not specified	Uncertain significance (Nov 12, 2021)
2-200419313-G-T		not specified	Uncertain significance (Feb 07, 2023)
2-200419320-G-T		not specified	Uncertain significance (Mar 12, 2024)
2-200419323-C-G		not specified	Uncertain significance (Mar 23, 2023)
2-200419344-C-T		not specified	Uncertain significance (Sep 29, 2023)
2-200419387-G-C		not specified	Uncertain significance (Dec 03, 2021)
2-200419469-C-T		not specified	Uncertain significance (Mar 27, 2023)
2-200419490-G-A		not specified	Uncertain significance (Jul 11, 2023)
2-200439125-G-A			Likely benign (Jun 21, 2018)
2-200439194-G-C		not specified	Uncertain significance (Apr 20, 2023)
2-200440714-G-A		not specified	Uncertain significance (Aug 08, 2022)
2-200440744-G-A		not specified	Uncertain significance (Aug 30, 2021)
2-200459789-C-T		not specified	Uncertain significance (Dec 19, 2022)
2-200467307-C-T		not specified	Uncertain significance (Feb 27, 2024)
2-200467367-A-T		not specified	Uncertain significance (May 09, 2023)
2-200469956-G-A		not specified	Uncertain significance (Oct 29, 2021)
2-200469960-C-T		not specified	Uncertain significance (Dec 15, 2023)
2-200469989-A-G		not specified	Uncertain significance (Jul 25, 2023)
2-200472916-G-A		not specified	Uncertain significance (Sep 13, 2023)
2-200472985-C-G		not specified	Uncertain significance (Jan 03, 2024)
2-200477638-T-G		not specified	Uncertain significance (Nov 30, 2022)
2-200477640-G-C		not specified	Uncertain significance (Oct 03, 2023)
2-200477657-C-T		not specified	Uncertain significance (Feb 16, 2023)
2-200477759-C-A		not specified	Uncertain significance (Sep 14, 2023)
2-200477762-G-A		not specified	Uncertain significance (Dec 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPATS2L	protein_coding	protein_coding	ENST00000358677	11	176383

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.558	0.442	124629	0	8	124637	0.0000321

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.31	243	308	0.790	0.0000176	3648
Missense in Polyphen		79	128.37	0.61541		1586
Synonymous	0.200	121	124	0.977	0.00000803	1069
Loss of Function	3.62	5	24.2	0.206	0.00000110	325

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000584	0.0000584
Ashkenazi Jewish	0.000101	0.0000994
East Asian	0.00	0.00
Finnish	0.0000464	0.0000464
European (Non-Finnish)	0.0000267	0.0000265
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000166	0.000165

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.0568
• rvis_EVS: 0.17
• rvis_percentile_EVS: 65.96

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.501
• ghis: 0.483

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.929

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Spats2l

Gene ontology

• Cellular component: nucleus;nucleolus;cytoplasm;cytosol;protein-containing complex
• Molecular function: RNA binding