SAC3D1

SAC3 domain containing 1

Basic information

Region (hg38): 11:65040901-65044828

Links

ENSG00000168061 ∙ NCBI:29901 ∙ OMIM:618796 ∙ HGNC:30179 ∙ Uniprot:A6NKF1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SAC3D1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SAC3D1 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			34	4		38
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	34	4	0

Variants in SAC3D1

This is a list of pathogenic ClinVar variants found in the SAC3D1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
11-65041314-G-A		not specified	Uncertain significance (Dec 25, 2024)
11-65041353-G-A		not specified	Uncertain significance (Jan 18, 2025)
11-65041353-G-C		not specified	Uncertain significance (Dec 19, 2022)
11-65041387-T-G		not specified	Uncertain significance (Jun 25, 2024)
11-65041430-T-A		not specified	Uncertain significance (Mar 06, 2025)
11-65041522-C-T		not specified	Uncertain significance (Nov 21, 2024)
11-65041554-G-C		not specified	Uncertain significance (Jan 20, 2025)
11-65041569-G-T		not specified	Likely benign (Dec 03, 2021)
11-65041576-C-T		not specified	Uncertain significance (Jan 04, 2022)
11-65041591-T-G		not specified	Uncertain significance (Nov 13, 2023)
11-65041647-G-A		not specified	Uncertain significance (Mar 08, 2024)
11-65041653-G-A		not specified	Uncertain significance (Oct 14, 2023)
11-65041662-G-A		not specified	Uncertain significance (Aug 17, 2022)
11-65041689-C-A		not specified	Uncertain significance (Mar 08, 2025)
11-65041732-G-A		not specified	Uncertain significance (Dec 17, 2023)
11-65041740-G-A		not specified	Uncertain significance (Aug 01, 2024)
11-65041797-T-C		not specified	Uncertain significance (Mar 20, 2024)
11-65041806-G-A		not specified	Likely benign (Jan 23, 2023)
11-65041845-C-T		not specified	Uncertain significance (Jul 19, 2023)
11-65041857-T-A		not specified	Uncertain significance (Feb 16, 2023)
11-65041858-A-G		not specified	Uncertain significance (Jun 01, 2023)
11-65044236-G-T		not specified	Uncertain significance (Jan 17, 2024)
11-65044272-C-T		not specified	Uncertain significance (Aug 20, 2024)
11-65044278-T-C		not specified	Uncertain significance (Dec 21, 2023)
11-65044291-G-A		not specified	Uncertain significance (Feb 12, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SAC3D1	protein_coding	protein_coding	ENST00000398846	2	3928

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000575	0.489	124779	0	15	124794	0.0000601

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.600	137	158	0.866	0.0000104	2127
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000869	0.0000869
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000558	0.0000556
Finnish	0.0000465	0.0000464
European (Non-Finnish)	0.0000889	0.0000795
Middle Eastern	0.0000558	0.0000556
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in centrosome duplication and mitotic progression. {ECO:0000250}.
• Pathway: miR-targeted genes in leukocytes - TarBase;miR-targeted genes in lymphocytes - TarBase (Consensus)

Recessive Scores

• pRec: 0.109

Haploinsufficiency Scores

• pHI: 0.100
• hipred: Y
• hipred_score: 0.506
• ghis: 0.411

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• gene_indispensability_pred: N
• gene_indispensability_score: 0.264

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sac3d1
• Phenotype: endocrine/exocrine gland phenotype; hematopoietic system phenotype; immune system phenotype

Gene ontology

• Biological process: cell cycle;spindle assembly;centrosome duplication;cell division
• Cellular component: nucleus;cytoplasm;centrosome;microtubule organizing center;spindle
• Molecular function: protein binding