RECK

reversion inducing cysteine rich protein with kazal motifs

Basic information

Region (hg38): 9:36036912-36124455

Previous symbols: [ "ST15" ]

Links

ENSG00000122707 ∙ NCBI:8434 ∙ OMIM:605227 ∙ HGNC:11345 ∙ Uniprot:O95980 ∙ 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 RECK gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RECK 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			53	4		57
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					2	2
non coding						0
Total	0	0	53	5	1

Variants in RECK

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

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

Position	Type	Phenotype	Significance	ClinVar
9-36037057-G-T		not specified	Uncertain significance (Jan 27, 2022)
9-36037059-G-T		not specified	Uncertain significance (Mar 01, 2023)
9-36037078-G-T		not specified	Uncertain significance (Sep 22, 2023)
9-36037093-G-A		not specified	Uncertain significance (Jun 29, 2023)
9-36052307-G-A		not specified	Uncertain significance (Apr 11, 2023)
9-36052312-G-A		not specified	Uncertain significance (Jun 16, 2023)
9-36058819-T-G			Benign (Dec 31, 2019)
9-36058868-G-T		not specified	Uncertain significance (Feb 23, 2023)
9-36060123-A-C		not specified	Uncertain significance (May 11, 2022)
9-36060129-G-C		not specified	Uncertain significance (Nov 09, 2021)
9-36063821-G-C		not specified	Uncertain significance (Jul 09, 2021)
9-36080611-C-G		not specified	Uncertain significance (Oct 13, 2023)
9-36087714-G-A		not specified	Uncertain significance (Mar 11, 2024)
9-36087753-C-G		not specified	Uncertain significance (Jun 10, 2024)
9-36087798-G-A		not specified	Uncertain significance (Feb 09, 2023)
9-36087897-C-T		not specified	Uncertain significance (May 30, 2024)
9-36087925-T-G		not specified	Uncertain significance (Jul 16, 2021)
9-36091180-C-T		not specified	Uncertain significance (Feb 21, 2024)
9-36091228-C-T		not specified	Uncertain significance (Jul 14, 2021)
9-36091291-C-A		not specified	Uncertain significance (Dec 28, 2023)
9-36100391-G-C		not specified	Uncertain significance (Nov 05, 2021)
9-36100453-A-T		not specified	Uncertain significance (Mar 04, 2024)
9-36100465-C-A		not specified	Uncertain significance (Oct 12, 2022)
9-36100479-G-A		not specified	Uncertain significance (Sep 17, 2021)
9-36102091-A-C			Benign (Jan 08, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RECK	protein_coding	protein_coding	ENST00000377966	21	88019

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.93e-10	1.00	125686	0	62	125748	0.000247

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.54	425	524	0.811	0.0000273	6390
Missense in Polyphen		80	126.43	0.63278		1535
Synonymous	0.156	184	187	0.986	0.0000102	1802
Loss of Function	3.47	25	52.0	0.481	0.00000267	646

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000178	0.000178
Ashkenazi Jewish	0.00	0.00
East Asian	0.000330	0.000326
Finnish	0.000185	0.000185
European (Non-Finnish)	0.000248	0.000246
Middle Eastern	0.000330	0.000326
South Asian	0.000558	0.000555
Other	0.000338	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Negatively regulates matrix metalloproteinase-9 (MMP-9) by suppressing MMP-9 secretion and by direct inhibition of its enzymatic activity. RECK down-regulation by oncogenic signals may facilitate tumor invasion and metastasis. Appears to also regulate MMP-2 and MT1-MMP, which are involved in cancer progression.
• Pathway: MicroRNAs in cancer - Homo sapiens (human);inhibition of matrix metalloproteinases;Post-translational modification: synthesis of GPI-anchored proteins;Post-translational protein modification;Metabolism of proteins (Consensus)

Recessive Scores

• pRec: 0.200

Intolerance Scores

• loftool: 0.778
• rvis_EVS: -0.95
• rvis_percentile_EVS: 9.27

Haploinsufficiency Scores

• pHI: 0.373
• hipred: Y
• hipred_score: 0.648
• ghis: 0.595

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0936

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Reck
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); limbs/digits/tail phenotype; skeleton phenotype; embryo phenotype; liver/biliary system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); 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); cellular phenotype; growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan)

Zebrafish Information Network

• Gene name: reck
• Affected structure: parachordal vessel
• Phenotype tag: abnormal
• Phenotype quality: absent

Gene ontology

• Biological process: vasculature development;blood vessel maturation;sprouting angiogenesis;embryo implantation;extracellular matrix organization;negative regulation of cell migration;embryonic forelimb morphogenesis;regulation of angiogenesis;canonical Wnt signaling pathway;regulation of establishment of blood-brain barrier;positive regulation of canonical Wnt signaling pathway;negative regulation of metalloendopeptidase activity
• Cellular component: extracellular region;plasma membrane;membrane;anchored component of membrane;Wnt signalosome
• Molecular function: endopeptidase inhibitor activity;serine-type endopeptidase inhibitor activity;protein binding;metalloendopeptidase inhibitor activity;Wnt-protein binding;coreceptor activity involved in canonical Wnt signaling pathway