SPIN2B

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

Basic information

Region (hg38): X:57118551-57121548

Links

ENSG00000186787 ∙ NCBI:474343 ∙ OMIM:300517 ∙ HGNC:33147 ∙ Uniprot:Q9BPZ2 ∙ 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 SPIN2B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPIN2B 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			4			4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	4	1	0

Variants in SPIN2B

This is a list of pathogenic ClinVar variants found in the SPIN2B 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-57119991-A-T		not specified	Uncertain significance (Jun 29, 2023)
X-57120196-T-C		not specified	Uncertain significance (Oct 26, 2022)
X-57120420-T-G			Likely benign (Oct 01, 2022)
X-57120433-G-A		not specified	Uncertain significance (Jul 16, 2024)
X-57120448-C-G		not specified	Uncertain significance (Sep 02, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPIN2B	protein_coding	protein_coding	ENST00000333933	1	2997

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0569	0.725	125593	0	2	125595	0.00000796

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.73	34	76.6	0.444	0.00000535	1695
Missense in Polyphen		7	24.879	0.28137		553
Synonymous	-0.199	30	28.6	1.05	0.00000213	502
Loss of Function	0.769	2	3.57	0.561	2.57e-7	95

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000760	0.0000760
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: Involved in the regulation of cell cycle progression, this activity is related to the inhibition of apoptosis following the removal of essential growth factors (PubMed:12145692). Exhibits H3K4me3-binding activity (PubMed:29061846). {ECO:0000269|PubMed:12145692, ECO:0000269|PubMed:29061846}.

Recessive Scores

• pRec: 0.119

Haploinsufficiency Scores

• pHI: 0.275
• hipred: N
• hipred_score: 0.218
• ghis: 0.553

Essentials

• essential_gene_CRISPR: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Low	Low	Low
Primary Immunodeficiency	Low	Low	Low
Cancer	Low	Low	Low

Mouse Genome Informatics

• Gene name: Spin2-ps4

Gene ontology

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