SPIN4

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

Basic information

Region (hg38): X:63347227-63351332

Links

ENSG00000186767 ∙ NCBI:139886 ∙ ∙ HGNC:27040 ∙ Uniprot:Q56A73 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Lui-Jee-Baron syndrome	XL	General	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	Craniofacial; Gastrointestinal; Neurologic	36927955

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SPIN4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPIN4 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			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	0	0

Variants in SPIN4

This is a list of pathogenic ClinVar variants found in the SPIN4 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-63350108-T-C		not specified	Uncertain significance (May 28, 2023)
X-63350270-A-G		not specified	Uncertain significance (Sep 26, 2023)
X-63350506-ACT-A		Lui-Jee-Baron syndrome	Pathogenic (Dec 18, 2023)
X-63350551-T-C		not specified	Uncertain significance (May 17, 2023)
X-63350707-C-T		not specified	Uncertain significance (Apr 25, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPIN4	protein_coding	protein_coding	ENST00000335144	1	4117

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.758	0.233	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.58	54	98.1	0.551	0.00000669	1628
Missense in 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

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: Exhibits H3K4me3-binding activity. {ECO:0000269|PubMed:29061846}.

Intolerance Scores

• rvis_EVS: -0.01
• rvis_percentile_EVS: 52.85

Haploinsufficiency Scores

• pHI: 0.238
• hipred: Y
• hipred_score: 0.516
• ghis: 0.524

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.307

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Spin4

Gene ontology

• Biological process: gamete generation
• Cellular component: nucleoplasm;cytosol
• Molecular function: protein binding;methylated histone binding