ST7L

protein-coding

suppression of tumorigenicity 7 like

Gene summary

This gene was identified by its similarity to the ST7 tumor suppressor gene found in the chromosome 7q31 region. This gene is clustered in a tail-to-tail manner with the WNT2B gene in a chromosomal region known to be deleted and rearranged in a variety of cancers. Several transcript variants encoding many different isoforms have been described, but some have not been fully characterized. [provided by RefSeq, Feb 2011]

MANE transcript

NM_017744.5

Inheritance

—

ClinVar variants

U:61B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.59

Max pathogenic AF

—

Genomic locus

chr1:112,523,514-112,620,825

External References & Databases

Ensembl (ENSG00000007341)

Transcript & Mutation Effects

hg38 • Region Span ~97.3 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 ST7L variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 55

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_017744.5. 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			1 clinvar			1
missense			57 clinvar	3 clinvar	2 clinvar	62
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	61	3	2	66

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 109 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_017744.5	RefSeq	NP_060214.2	15	MANE Select
ENST00000358039.9	Ensembl	ENSP00000350734.4	15	MANE Select
NM_001308264.2	RefSeq	NP_001295193.1	11	Standard
NM_138727.4	RefSeq	NP_620055.1	15	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

negative regulation of cell growth

Cellular Component

integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000358039
Coding exons: 15
Length: 97308
Individuals with no LoFs: 125649
Homozygous LoFs: 2
Heterozygous LoFs: 96
Defined: 125747
p: 0.000390

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.583	264	292	0.904	0.0000134	3692
Missense (PolyPhen)		131	143.85	0.91069		1904
Synonymous	-0.0983	109	108	1.01	0.00000505	1112
Loss of Function	2.14	19	32.1	0.592	0.00000152	420

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00037	0.00031	rare
Latino/Admixed American	0.00069	0.00067	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00027	0.00027	rare
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.00043	0.00042	rare
South Asian	0.00051	0.00046	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.990
RVIS EVS: 1.91
RVIS percentile EVS: 97.39

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0461

Gene Damage Prediction

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