SCAI

suppressor of cancer cell invasion

Basic information

Region (hg38): 9:124942607-125143528

Previous symbols: [ "C9orf126" ]

Links

ENSG00000173611 ∙ NCBI:286205 ∙ OMIM:619222 ∙ HGNC:26709 ∙ Uniprot:Q8N9R8 ∙ 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 SCAI gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SCAI 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			19			19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	19	0	0

Variants in SCAI

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

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

Position	Type	Phenotype	Significance	ClinVar
9-124952878-G-T		not specified	Uncertain significance (Apr 06, 2023)
9-124952890-G-T		not specified	Uncertain significance (Jul 07, 2022)
9-124971411-T-C		not specified	Uncertain significance (Oct 26, 2022)
9-124971453-A-G		not specified	Uncertain significance (Oct 18, 2021)
9-124971679-C-T		not specified	Uncertain significance (Jun 14, 2023)
9-124971686-G-A		not specified	Uncertain significance (Apr 12, 2024)
9-124971709-C-T		not specified	Uncertain significance (Sep 07, 2022)
9-124971793-A-G		not specified	Uncertain significance (May 21, 2024)
9-124971815-G-A		not specified	Uncertain significance (Nov 20, 2023)
9-124976185-T-C		not specified	Uncertain significance (Dec 06, 2022)
9-125001979-C-T		not specified	Uncertain significance (Aug 23, 2021)
9-125002030-T-C		not specified	Uncertain significance (Jan 10, 2022)
9-125003487-C-G		not specified	Uncertain significance (Jul 25, 2023)
9-125003528-G-C		not specified	Uncertain significance (Feb 28, 2023)
9-125018822-T-C		not specified	Uncertain significance (Dec 16, 2023)
9-125018829-G-C		not specified	Uncertain significance (Jun 07, 2023)
9-125019171-C-T		not specified	Uncertain significance (Feb 11, 2022)
9-125020760-C-A		not specified	Uncertain significance (Feb 22, 2023)
9-125028461-C-A		not specified	Uncertain significance (Dec 23, 2023)
9-125029739-T-C		not specified	Likely benign (Jan 22, 2024)
9-125055885-T-C		not specified	Uncertain significance (Mar 29, 2022)
9-125055978-G-T		not specified	Uncertain significance (Mar 28, 2024)
9-125142657-T-C		not specified	Uncertain significance (Sep 29, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SCAI	protein_coding	protein_coding	ENST00000373549	19	200899

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.000645	124782	0	5	124787	0.0000200

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.01	178	332	0.535	0.0000176	4104
Missense in Polyphen		23	82.655	0.27826		1004
Synonymous	0.456	112	118	0.947	0.00000605	1178
Loss of Function	5.39	5	43.2	0.116	0.00000255	487

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000935	0.0000935
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000595	0.0000556
Finnish	0.00	0.00
European (Non-Finnish)	0.0000181	0.0000177
Middle Eastern	0.0000595	0.0000556
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Tumor suppressor which functions to suppress MRTFA- induced SRF transcriptional activity. May function in the RHOA- DIAPH1 signal transduction pathway and regulate cell migration through transcriptional regulation of ITGB1. {ECO:0000269|PubMed:19350017}.
• Pathway: Signal Transduction;RHO GTPases Activate Formins;RHO GTPase Effectors;Signaling by Rho GTPases;RhoA signaling pathway (Consensus)

Recessive Scores

• pRec: 0.0917

Intolerance Scores

• loftool: 0.321
• rvis_EVS: -0.49
• rvis_percentile_EVS: 22.36

Haploinsufficiency Scores

• pHI: 0.186
• hipred: Y
• hipred_score: 0.617
• ghis: 0.602

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.231

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Scai
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype; cellular phenotype; endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: transcription, DNA-templated;negative regulation of cell migration;negative regulation of Rho protein signal transduction;negative regulation of nucleic acid-templated transcription
• Cellular component: nucleus;nucleoplasm;cytoplasm;integral component of membrane;nuclear membrane
• Molecular function: transcription corepressor activity;protein binding