SPC24

protein-coding

SPC24 component of NDC80 kinetochore complex, the group of NDC80 kinetochore complex

Gene summary

Predicted to contribute to microtubule binding activity. Involved in attachment of spindle microtubules to kinetochore. Located in kinetochore; nucleolus; and nucleoplasm. Part of Ndc80 complex. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

SPBC24

MANE transcript

NM_182513.4

Inheritance

—

ClinVar variants

U:20B:2

Top phenotype

SPC24-related disorder

gnomAD constraint

pLI —, LoF o/e 0.71

Max pathogenic AF

—

Genomic locus

chr19:11,131,520-11,155,807

External References & Databases

Ensembl (ENSG00000161888)

Transcript & Mutation Effects

hg38 • Region Span ~24.3 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 SPC24 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 22

SPC24-related disorderTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_182513.4. 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						0
missense			20 clinvar	2 clinvar		22
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	20	2	0	22

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 23 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_182513.4	RefSeq	NP_872319.1	5	MANE Select
ENST00000592540.6	Ensembl	ENSP00000465075.1	5	MANE Select
NM_001317031.2	RefSeq	NP_001303960.1	5	Standard
NM_001317032.2	RefSeq	NP_001303961.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Signal Transduction
Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal
Amplification of signal from the kinetochores
Mitotic Spindle Checkpoint
Cell Cycle Checkpoints

Biological Process

cell cycle
cell division

Molecular Function

protein binding

Cellular Component

condensed chromosome kinetochore
nucleus
nucleolus
cytosol
Ndc80 complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000592540
Coding exons: 5
Length: 24289
Individuals with no LoFs: 124612
Homozygous LoFs: 0
Heterozygous LoFs: 8
Defined: 124620
p: 0.0000321

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.709	78	97.7	0.798	0.00000517	1251
Missense (PolyPhen)		21	29.314	0.71639		389
Synonymous	1.18	33	42.9	0.770	0.00000261	359
Loss of Function	0.834	7	9.82	0.713	5.03e-7	108

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000065	0.000065	rare
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000036	0.000035	rare
South Asian	0	0.0	absent
Other	0.00017	0.00017	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Acts as a component of the essential kinetochore- associated NDC80 complex, which is required for chromosome segregation and spindle checkpoint activity (PubMed:14738735). Required for kinetochore integrity and the organization of stable microtubule binding sites in the outer plate of the kinetochore (PubMed:14738735). The NDC80 complex synergistically enhances the affinity of the SKA1 complex for microtubules and may allow the NDC80 complex to track depolymerizing microtubules (PubMed:23085020). {ECO:0000269|PubMed:14738735, ECO:0000269|PubMed:23085020}.;

Recessive Scores

pRec: 0.119

Intolerance Scores

LoFtool: 0.522
RVIS EVS: 0.41
RVIS percentile EVS: 76.67

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.945

Gene Damage Prediction

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