SAC3D1

protein-coding

SAC3 domain containing 1

Gene summary

Predicted to be involved in centrosome duplication and spindle assembly. Predicted to act upstream of or within negative regulation of receptor signaling pathway via JAK-STAT and regulation of immune response. Predicted to be located in microtubule cytoskeleton. Predicted to be part of protein-containing complex. Predicted to be active in centrosome; nucleus; and spindle. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_013299.4

Inheritance

—

ClinVar variants

U:70B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.9

Max pathogenic AF

—

Genomic locus

chr11:65,040,901-65,044,828

External References & Databases

Ensembl (ENSG00000168061)

Transcript & Mutation Effects

hg38 • Region Span ~3.9 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 SAC3D1 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 76

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_013299.4. 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			70 clinvar	6 clinvar		76
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	70	6	0	76

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 15 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_013299.4	RefSeq	NP_037431.3	2	MANE Select
ENST00000652489.1	Ensembl	ENSP00000499090.1	2	MANE Select
NM_001367485.1	RefSeq	NP_001354414.1	2	Standard
NM_001367486.1	RefSeq	NP_001354415.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

miR-targeted genes in leukocytes - TarBase
miR-targeted genes in lymphocytes - TarBase

Biological Process

cell cycle
spindle assembly
centrosome duplication
cell division

Molecular Function

protein binding

Cellular Component

nucleus
cytoplasm
centrosome
microtubule organizing center
spindle

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000398846
Coding exons: 2
Length: 3928
Individuals with no LoFs: 124779
Homozygous LoFs: 0
Heterozygous LoFs: 15
Defined: 124794
p: 0.0000601

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.600	137	158	0.866	0.0000104	2127
Missense (PolyPhen)		60	68.812	0.87194		1011
Synonymous	-0.240	73	70.4	1.04	0.00000443	805
Loss of Function	0.219	5	5.56	0.900	3.29e-7	74

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000087	0.000087	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000056	0.000056	rare
Finnish	0.000047	0.000046	rare
European (Non-Finnish)	0.000089	0.000079	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Involved in centrosome duplication and mitotic progression. {ECO:0000250}.;

Recessive Scores

pRec: 0.109

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Indispensability pred.: N
Indispensability score: 0.264

Gene Damage Prediction

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