SPATA2L

spermatogenesis associated 2 like

Basic information

Region (hg38): 16:89696357-89701705

Previous symbols: [ "C16orf76" ]

Links

ENSG00000158792 ∙ NCBI:124044 ∙ ∙ HGNC:28393 ∙ Uniprot:Q8IUW3 ∙ 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 SPATA2L gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPATA2L 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			47	2		49
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	47	2	0

Variants in SPATA2L

This is a list of pathogenic ClinVar variants found in the SPATA2L region.

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

Position	Type	Phenotype	Significance	ClinVar
16-89697341-C-G		not specified	Uncertain significance (Jan 09, 2024)
16-89697399-G-A		not specified	Uncertain significance (Dec 13, 2022)
16-89697402-G-A		not specified	Uncertain significance (Jan 16, 2025)
16-89697408-C-T		not specified	Likely benign (May 05, 2023)
16-89697425-C-A		not specified	Uncertain significance (Apr 04, 2023)
16-89697425-C-T		not specified	Uncertain significance (Jul 12, 2023)
16-89697426-G-A		not specified	Uncertain significance (Jun 16, 2023)
16-89697443-C-T		not specified	Uncertain significance (Feb 21, 2024)
16-89697507-T-C		not specified	Uncertain significance (Dec 10, 2024)
16-89697522-G-A		not specified	Uncertain significance (Aug 21, 2023)
16-89697560-G-A		not specified	Uncertain significance (Mar 04, 2024)
16-89697563-A-G		not specified	Uncertain significance (Jul 26, 2024)
16-89697579-A-T		not specified	Uncertain significance (Feb 05, 2025)
16-89697591-C-T		not specified	Uncertain significance (Jun 13, 2024)
16-89697599-C-T		not specified	Uncertain significance (Dec 11, 2023)
16-89697600-G-A		not specified	Uncertain significance (May 23, 2023)
16-89697603-T-C		not specified	Uncertain significance (Jul 27, 2021)
16-89697605-C-T		not specified	Likely benign (Sep 14, 2022)
16-89697606-G-A		not specified	Uncertain significance (Apr 22, 2024)
16-89697611-G-A		not specified	Uncertain significance (Aug 19, 2024)
16-89697668-C-T		not specified	Uncertain significance (Oct 27, 2023)
16-89697671-C-T		not specified	Uncertain significance (Aug 02, 2021)
16-89697692-G-A		not specified	Uncertain significance (Nov 12, 2024)
16-89697752-G-A		not specified	Uncertain significance (Jul 07, 2024)
16-89697761-T-C		not specified	Uncertain significance (Sep 20, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPATA2L	protein_coding	protein_coding	ENST00000289805	2	5363

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0406	0.933	125458	0	17	125475	0.0000677

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.256	265	254	1.05	0.0000163	2602
Missense in Polyphen		59	81.393	0.72488		944
Synonymous	-3.26	161	116	1.38	0.00000747	968
Loss of Function	1.92	4	10.8	0.370	5.44e-7	122

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000226	0.000214
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000112	0.000106
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000172	0.000163

dbNSFP

Source: dbNSFP

• Pathway: Necroptosis - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.110

Haploinsufficiency Scores

• pHI: 0.132
• hipred: N
• hipred_score: 0.248
• ghis: 0.499

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.901

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Spata2l