ST7

suppression of tumorigenicity 7, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 7:116953237-117230176

Previous symbols: [ "FAM4A1" ]

Links

ENSG00000004866 ∙ NCBI:7982 ∙ OMIM:600833 ∙ HGNC:11351 ∙ Uniprot:Q9NRC1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• developmental and epileptic encephalopathy (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ST7 gene.

• Inborn genetic diseases (7 variants)
• not provided (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ST7 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				1	1	2
missense			7	1		8
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	7	2	1

Variants in ST7

This is a list of pathogenic ClinVar variants found in the ST7 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-116953551-C-T		not specified	Uncertain significance (Apr 07, 2022)
7-116953586-A-C		not specified	Uncertain significance (Mar 02, 2023)
7-116953637-T-C		not specified	Uncertain significance (Dec 05, 2022)
7-116953668-A-C		not specified	Uncertain significance (Jan 30, 2024)
7-116953685-A-C		not specified	Uncertain significance (Dec 28, 2023)
7-117130530-T-G		Global developmental delay;Intractable seizure;Brain atrophy	Likely pathogenic (Dec 01, 2014)
7-117130581-G-A			Benign (Dec 31, 2019)
7-117130604-C-G		not specified	Uncertain significance (Oct 05, 2023)
7-117136188-G-A		not specified	Uncertain significance (Mar 23, 2022)
7-117136204-A-G			Likely benign (Dec 31, 2019)
7-117138501-G-A		not specified	Uncertain significance (Jan 23, 2024)
7-117138504-C-T		not specified	Uncertain significance (Aug 22, 2023)
7-117170983-T-C		ST7-related disorder	Benign (Oct 22, 2019)
7-117209927-G-A		ST7-related disorder	Likely benign (Oct 01, 2019)
7-117219076-G-A		ST7-related disorder	Likely benign (Mar 03, 2020)
7-117219162-G-A		not specified	Uncertain significance (Jan 04, 2024)
7-117221923-C-T		not specified	Uncertain significance (Dec 11, 2023)
7-117222070-T-C			Benign (Mar 05, 2018)
7-117222921-C-T		not specified	Uncertain significance (May 03, 2023)
7-117222922-G-T			Likely benign (Dec 31, 2019)
7-117222949-C-T		not specified	Uncertain significance (Mar 29, 2022)
7-117222979-G-T		ST7-related disorder	Likely benign (May 31, 2022)
7-117229759-C-A		ST7-related disorder	Likely benign (May 31, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ST7	protein_coding	protein_coding	ENST00000265437	16	276866

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.997	0.00297	125739	0	8	125747	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.38	145	313	0.463	0.0000156	3820
Missense in Polyphen		58	164.16	0.35331		2012
Synonymous	0.419	108	114	0.950	0.00000571	1107
Loss of Function	4.83	4	34.7	0.115	0.00000183	414

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.0000996	0.0000992
East Asian	0.00	0.00
Finnish	0.000139	0.000139
European (Non-Finnish)	0.0000283	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.0000367	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May act as a tumor suppressor. {ECO:0000269|PubMed:16474848}.

Recessive Scores

• pRec: 0.115

Intolerance Scores

• loftool: 0.449
• rvis_EVS: -0.25
• rvis_percentile_EVS: 35.99

Haploinsufficiency Scores

• pHI: 0.186
• hipred: Y
• hipred_score: 0.727
• ghis: 0.612

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.801

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: St7

Gene ontology

• Biological process: extracellular matrix organization;regulation of cell differentiation
• Cellular component: integral component of membrane