SASS6

SAS-6 centriolar assembly protein

Basic information

Region (hg38): 1:100083563-100132955

Links

ENSG00000156876 ∙ NCBI:163786 ∙ OMIM:609321 ∙ HGNC:25403 ∙ Uniprot:Q6UVJ0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• microcephaly 14, primary, autosomal recessive (Moderate), mode of inheritance: AR
• autosomal recessive primary microcephaly (Supportive), mode of inheritance: AR
• microcephaly 14, primary, autosomal recessive (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Microcephaly 14, primary, autosomal recessive	AR	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	Neurologic	24951542; 30639237

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SASS6 gene.

• Inborn genetic diseases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SASS6 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				5	5	10
missense			44	8	2	54
nonsense		1				1
start loss						0
frameshift	1	2	1			4
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2	3	5
non coding		1		3	28	32
Total	1	4	45	16	35

Highest pathogenic variant AF is 0.00000658

Variants in SASS6

This is a list of pathogenic ClinVar variants found in the SASS6 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-100085359-G-C		Inborn genetic diseases	Uncertain significance (Jul 22, 2024)
1-100085367-C-T			Benign (Dec 31, 2019)
1-100085381-C-T			Likely benign (Apr 07, 2018)
1-100085428-T-G		Inborn genetic diseases	Uncertain significance (Dec 02, 2022)
1-100085534-A-T		Microcephaly 14, primary, autosomal recessive	Pathogenic (Sep 10, 2020)
1-100085568-C-T		not specified • Microcephaly 14, primary, autosomal recessive	Benign (Apr 11, 2023)
1-100085569-G-A		Inborn genetic diseases	Uncertain significance (Oct 29, 2021)
1-100085620-C-T		Inborn genetic diseases	Uncertain significance (Sep 14, 2023)
1-100085634-A-C		not specified	Conflicting classifications of pathogenicity (Dec 31, 2019)
1-100085885-A-G			Benign (Jun 19, 2021)
1-100088182-A-C		Inborn genetic diseases	Uncertain significance (Oct 16, 2023)
1-100088219-C-T			Likely benign (Dec 07, 2018)
1-100088223-A-G		Inborn genetic diseases	Uncertain significance (Oct 01, 2024)
1-100102675-CA-C			Benign (Jun 20, 2021)
1-100102675-C-CA			Benign (Jun 19, 2021)
1-100102675-C-CAA			Benign (Jun 20, 2021)
1-100102952-T-C			Likely benign (May 15, 2018)
1-100102962-C-T		Inborn genetic diseases	Uncertain significance (Aug 02, 2021)
1-100102998-G-A		Inborn genetic diseases	Uncertain significance (Sep 24, 2024)
1-100103049-A-G		Inborn genetic diseases	Uncertain significance (Aug 05, 2024)
1-100103058-G-C		not specified	Uncertain significance (Sep 29, 2016)
1-100103203-C-G			Benign (Jun 19, 2021)
1-100105452-G-A			Benign (Jun 20, 2021)
1-100105769-C-T		Inborn genetic diseases	Uncertain significance (Sep 01, 2021)
1-100105801-G-A		Inborn genetic diseases	Uncertain significance (Jan 23, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SASS6	protein_coding	protein_coding	ENST00000287482	17	49393

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.74e-7	1.00	125647	1	99	125747	0.000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.01	261	311	0.839	0.0000150	4277
Missense in Polyphen		38	65.64	0.57892		965
Synonymous	-0.239	123	120	1.03	0.00000607	1185
Loss of Function	3.15	18	39.3	0.458	0.00000192	507

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000400	0.000395
Ashkenazi Jewish	0.00	0.00
East Asian	0.000235	0.000217
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.000416	0.000404
Middle Eastern	0.000235	0.000217
South Asian	0.00125	0.00111
Other	0.000848	0.000815

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Central scaffolding component of the centrioles ensuring their 9-fold symmetry. Required for centrosome biogenesis and duplication: required both for mother-centriole-dependent centriole duplication and deuterosome-dependent centriole amplification in multiciliated cells. Overexpression results in excess foci-bearing centriolar markers. Required for the recruitment of STIL to the procentriole and for STIL-mediated centriole amplification (PubMed:22020124). {ECO:0000269|PubMed:15665853, ECO:0000269|PubMed:16244668, ECO:0000269|PubMed:17681131, ECO:0000269|PubMed:22020124}.
• Disease: DISEASE: Microcephaly 14, primary, autosomal recessive (MCPH14) [MIM:616402]: A form of microcephaly, a disease defined as a head circumference more than 3 standard deviations below the age, sex and ethnically matched mean. Brain weight is markedly reduced and the cerebral cortex is disproportionately small. {ECO:0000269|PubMed:24951542}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Recessive Scores

• pRec: 0.0930

Intolerance Scores

• loftool: 0.675
• rvis_EVS: -0.25
• rvis_percentile_EVS: 36.07

Haploinsufficiency Scores

• pHI: 0.100
• hipred: N
• hipred_score: 0.476
• ghis: 0.635

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.955

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sass6

Zebrafish Information Network

• Gene name: sass6
• Affected structure: sperm
• Phenotype tag: abnormal
• Phenotype quality: composition

Gene ontology

• Biological process: centriole replication;centrosome duplication
• Cellular component: centrosome;centriole;microtubule organizing center;cytosol;deuterosome
• Molecular function: protein binding