SPIN2B

protein-coding

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

Gene summary

Enables histone H3K4me3 reader activity. Predicted to be involved in regulation of DNA-templated transcription. Predicted to be located in nucleus. Predicted to be active in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001006681.2

Inheritance

—

ClinVar variants

U:10B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.56

Max pathogenic AF

—

Genomic locus

chrX:57,118,551-57,121,548

External References & Databases

Ensembl (ENSG00000186787)

Transcript & Mutation Effects

hg38 • Region Span ~3.0 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SPIN2B variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 10

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001006681.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				2 clinvar		2
missense			10 clinvar	1 clinvar		11
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	10	3	0	13

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 41 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001006681.2	RefSeq	NP_001006682.1	1	MANE Select
ENST00000434397.3	Ensembl	ENSP00000404314.2	1	MANE Select
NM_001006682.2	RefSeq	NP_001006683.1	1	Standard
NM_001006683.2	RefSeq	NP_001006684.1	1	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

apoptotic process
cell cycle
gamete generation
regulation of cell cycle

Molecular Function

protein binding
methylated histone binding

Cellular Component

nucleoplasm
cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000333933
Coding exons: 1
Length: 2997
Individuals with no LoFs: 125593
Homozygous LoFs: 0
Heterozygous LoFs: 2
Defined: 125595
p: 0.00000796

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.73	34	76.6	0.444	0.00000535	1695
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000076	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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