SPIN2A

spindlin family member 2A, the group of Spindlin family|Tudor domain containing

Basic information

Region (hg38): X:57134530-57137523

Previous symbols: [ "SPIN2" ]

Links

ENSG00000147059 ∙ NCBI:54466 ∙ OMIM:300621 ∙ HGNC:20694 ∙ Uniprot:Q99865 ∙ 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 SPIN2A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPIN2A 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				1		1
missense			19	2		21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	3	0

Variants in SPIN2A

This is a list of pathogenic ClinVar variants found in the SPIN2A region.

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

Position	Type	Phenotype	Significance	ClinVar
X-57135841-C-G		not specified	Uncertain significance (Nov 23, 2022)
X-57135874-T-C		not specified	Uncertain significance (Feb 12, 2025)
X-57135888-G-A		not specified	Uncertain significance (May 10, 2024)
X-57135898-T-C		not specified	Likely benign (Jul 14, 2021)
X-57135901-C-T		not specified	Uncertain significance (Dec 23, 2024)
X-57135910-G-A		not specified	Uncertain significance (Jun 04, 2024)
X-57135915-A-G		not specified	Uncertain significance (Jan 26, 2022)
X-57135937-C-T		not specified	Uncertain significance (Jan 21, 2025)
X-57135969-A-G		not specified	Uncertain significance (May 28, 2024)
X-57135993-G-C		not specified	Uncertain significance (Jun 06, 2023)
X-57135997-C-T		not specified	Uncertain significance (Dec 15, 2024)
X-57136001-C-G		not specified	Uncertain significance (Mar 14, 2025)
X-57136033-T-C		not specified	Uncertain significance (Sep 24, 2024)
X-57136039-G-A		not specified	Uncertain significance (Apr 29, 2024)
X-57136047-C-T		not specified	Uncertain significance (Dec 16, 2024)
X-57136077-A-G		not specified	Uncertain significance (Nov 12, 2024)
X-57136089-G-T		not specified	Uncertain significance (Feb 21, 2024)
X-57136135-C-G		not specified	Uncertain significance (Feb 06, 2024)
X-57136186-C-G		not specified	Uncertain significance (Jan 18, 2025)
X-57136209-C-T		not specified	Uncertain significance (Aug 02, 2021)
X-57136260-C-G		not specified	Uncertain significance (Jun 16, 2022)
X-57136347-A-G		not specified	Uncertain significance (Apr 22, 2024)
X-57136365-A-G		not specified	Uncertain significance (May 31, 2023)
X-57136387-T-G		not specified	Uncertain significance (Jan 01, 2025)
X-57136388-T-G			Likely benign (Nov 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPIN2A	protein_coding	protein_coding	ENST00000374908	1	3096

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00115	0.406	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.03	100	74.8	1.34	0.00000517	1691
Missense in Polyphen		37	24.623	1.5027		558
Synonymous	-0.624	31	26.9	1.15	0.00000188	500
Loss of Function	-0.250	4	3.50	1.14	2.46e-7	94

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in the regulation of cell cycle progression (By similarity). Exhibits H3K4me3-binding activity (PubMed:29061846). {ECO:0000250|UniProtKB:Q9BPZ2, ECO:0000269|PubMed:29061846}.

Recessive Scores

• pRec: 0.121

Haploinsufficiency Scores

• pHI: 0.276
• hipred: N
• hipred_score: 0.187

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0902

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Spin2-ps4

Gene ontology

• Biological process: cell cycle;gamete generation;regulation of cell cycle
• Cellular component: cellular_component;nucleoplasm;cytosol
• Molecular function: molecular_function;protein binding;methylated histone binding