SPIN4

protein-coding

spindlin family member 4, the group of Spindlin family|Tudor domain containing

Gene summary

Enables histone H3K4me3 reader activity. Involved in negative regulation of cell population proliferation and positive regulation of canonical Wnt signaling pathway. Located in chromatin; cytoplasm; and nucleus. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001012968.3

Inheritance

ClinVar variants

P:1U:14B:1

Top phenotype

Lui-Jee-Baron syndrome

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chrX:63,347,228-63,351,332

External References & Databases

Ensembl (ENSG00000186767)

Transcript & Mutation Effects

hg38 • Region Span ~4.1 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

Lui-Jee-Baron syndromeMODERATE

Inheritance Pattern: XL

Disease ID:MONDO:0957919

Submitter: PanelApp Australia

Clinical Genomic Database (CGD)

Lui-Jee-Baron syndromeXL

Manifestation: Craniofacial; Gastrointestinal; Neurologic

Intervention: General

Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing

Refs: 36927955

Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SPIN4 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 12

not providedTotal: 2

Lui-Jee-Baron syndromeTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001012968.3. 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				1 clinvar		1
missense			14 clinvar			14
nonsense						0
start loss						0
frameshift	1 clinvar					1
splice donor/acceptor (+/-2bp)						0
Total	1	0	14	1	0	16

Highest pathogenic variant AF is 9.105809e-7

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 2 of 2 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001012968.3	RefSeq	NP_001012986.2	1	MANE Select
ENST00000374884.3	Ensembl	ENSP00000364018.3	1	MANE Select

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

gamete generation

Molecular Function

protein binding
methylated histone binding

Cellular Component

nucleoplasm
cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000335144
Coding exons: 1
Length: 4117
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.58	54	98.1	0.551	0.00000669	1628
Missense (PolyPhen)		9	33.527	0.26844		616
Synonymous	0.565	35	39.5	0.886	0.00000277	502
Loss of Function	2.01	0	4.70	0.00	3.01e-7	86

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
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: Exhibits H3K4me3-binding activity. {ECO:0000269|PubMed:29061846}.;

Intolerance Scores

RVIS EVS: -0.01
RVIS percentile EVS: 52.85

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: N
Indispensability score: 0.307

Gene Damage Prediction

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