SPATS1

spermatogenesis associated serine rich 1

Basic information

Region (hg38): 6:44342650-44380179

Links

ENSG00000249481 ∙ NCBI:221409 ∙ ∙ HGNC:22957 ∙ Uniprot:Q496A3 ∙ 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 SPATS1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPATS1 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			31			31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	31	0	0

Variants in SPATS1

This is a list of pathogenic ClinVar variants found in the SPATS1 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-44343111-C-T		not specified	Uncertain significance (Aug 04, 2023)
6-44352792-G-C		not specified	Uncertain significance (Dec 05, 2022)
6-44352792-G-T		not specified	Uncertain significance (May 10, 2024)
6-44352813-T-C		not specified	Uncertain significance (Mar 24, 2023)
6-44360463-A-T		not specified	Uncertain significance (Aug 12, 2024)
6-44360465-C-T		not specified	Uncertain significance (Dec 01, 2022)
6-44360466-G-A		not specified	Likely benign (Feb 19, 2025)
6-44360506-G-C		not specified	Uncertain significance (Oct 01, 2024)
6-44360508-C-T		not specified	Uncertain significance (Oct 04, 2024)
6-44360550-G-C		not specified	Uncertain significance (Feb 11, 2022)
6-44360559-A-C		not specified	Uncertain significance (Jan 23, 2024)
6-44361895-C-G		not specified	Uncertain significance (Aug 11, 2023)
6-44361899-G-A		not specified	Uncertain significance (Apr 23, 2024)
6-44361900-G-A		not specified	Uncertain significance (Jul 26, 2022)
6-44361908-T-C		not specified	Uncertain significance (May 05, 2022)
6-44361909-G-A		not specified	Uncertain significance (Sep 27, 2024)
6-44361932-G-A		not specified	Uncertain significance (Feb 21, 2024)
6-44361933-G-A		not specified	Uncertain significance (Jul 27, 2024)
6-44361936-A-G		not specified	Uncertain significance (Jul 07, 2024)
6-44361965-G-A		not specified	Uncertain significance (Jan 04, 2022)
6-44368411-A-G		not specified	Uncertain significance (Dec 21, 2022)
6-44368414-C-A		not specified	Uncertain significance (Sep 14, 2022)
6-44368417-G-C		not specified	Uncertain significance (Feb 28, 2025)
6-44368429-T-C		not specified	Uncertain significance (Jun 18, 2024)
6-44368435-T-C		not specified	Uncertain significance (Nov 09, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPATS1	protein_coding	protein_coding	ENST00000288390	8	34508

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.96e-7	0.534	125722	0	23	125745	0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.835	134	164	0.817	0.00000851	1983
Missense in Polyphen		43	49.525	0.86826		648
Synonymous	-0.651	67	60.6	1.11	0.00000336	550
Loss of Function	0.851	11	14.5	0.759	6.09e-7	191

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000362	0.000362
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000545	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000115	0.000114
Middle Eastern	0.0000545	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0806

Intolerance Scores

• loftool: 0.647
• rvis_EVS: 0.24
• rvis_percentile_EVS: 69.21

Haploinsufficiency Scores

• pHI: 0.0741
• hipred: N
• hipred_score: 0.153

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Spats1
• Phenotype: hematopoietic system phenotype