FERMT2

FERM domain containing kindlin 2, the group of FERM domain containing|Fermitins|Pleckstrin homology domain containing

Basic information

Region (hg38): 14:52857268-52952435

Previous symbols: [ "PLEKHC1" ]

Links

ENSG00000073712 ∙ NCBI:10979 ∙ OMIM:607746 ∙ HGNC:15767 ∙ Uniprot:Q96AC1 ∙ 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 FERMT2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FERMT2 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
missense			31	1		32
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	31	2	0

Variants in FERMT2

This is a list of pathogenic ClinVar variants found in the FERMT2 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-52858438-T-C		not specified	Uncertain significance (May 15, 2023)
14-52859658-C-A		not specified	Uncertain significance (Jul 05, 2023)
14-52859658-C-T		not specified	Uncertain significance (Dec 11, 2024)
14-52860347-A-C		not specified	Uncertain significance (Jan 27, 2025)
14-52860348-T-C		not specified	Uncertain significance (Aug 20, 2024)
14-52860350-A-G		not specified	Uncertain significance (Jan 23, 2023)
14-52861025-T-C		not specified	Likely benign (Oct 18, 2021)
14-52861030-C-G		not specified	Uncertain significance (Jan 18, 2025)
14-52861031-C-G		not specified	Uncertain significance (Apr 08, 2024)
14-52864426-T-C		not specified	Uncertain significance (Nov 28, 2024)
14-52864522-G-C		not specified	Uncertain significance (Nov 10, 2022)
14-52864561-G-A		not specified	Uncertain significance (Oct 26, 2021)
14-52864622-C-T		not specified	Uncertain significance (May 20, 2024)
14-52864823-G-A		not specified	Uncertain significance (Oct 06, 2022)
14-52872801-C-T		not specified	Uncertain significance (Jul 14, 2021)
14-52872825-G-A		not specified	Uncertain significance (Dec 09, 2024)
14-52872855-C-T		not specified	Uncertain significance (Jun 29, 2022)
14-52872891-T-C		not specified	Uncertain significance (Oct 04, 2024)
14-52872897-T-C		not specified	Uncertain significance (Jan 03, 2025)
14-52875228-T-C		not specified	Uncertain significance (Dec 06, 2024)
14-52875242-C-A		not specified	Uncertain significance (May 04, 2022)
14-52875242-C-T		not specified	Uncertain significance (Feb 19, 2025)
14-52875244-C-G			Likely benign (Apr 01, 2023)
14-52878652-G-C		not specified	Uncertain significance (Mar 22, 2023)
14-52881091-T-C		not specified	Uncertain significance (Feb 12, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FERMT2	protein_coding	protein_coding	ENST00000343279	15	95168

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000112	125712	0	2	125714	0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.96	258	363	0.711	0.0000173	4566
Missense in Polyphen		90	148.52	0.606		1899
Synonymous	0.250	122	126	0.972	0.00000614	1229
Loss of Function	5.44	1	36.4	0.0274	0.00000164	470

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000352	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Scaffolding protein that enhances integrin activation mediated by TLN1 and/or TLN2, but activates integrins only weakly by itself. Binds to membranes enriched in phosphoinositides. Enhances integrin-mediated cell adhesion onto the extracellular matrix and cell spreading; this requires both its ability to interact with integrins and with phospholipid membranes. Required for the assembly of focal adhesions. Participates in the connection between extracellular matrix adhesion sites and the actin cytoskeleton and also in the orchestration of actin assembly and cell shape modulation. Recruits FBLIM1 to focal adhesions. Plays a role in the TGFB1 and integrin signaling pathways. Stabilizes active CTNNB1 and plays a role in the regulation of transcription mediated by CTNNB1 and TCF7L2/TCF4 and in Wnt signaling. {ECO:0000269|PubMed:12679033, ECO:0000269|PubMed:18458155, ECO:0000269|PubMed:21325030, ECO:0000269|PubMed:22030399, ECO:0000269|PubMed:22078565, ECO:0000269|PubMed:22699938}.
• Pathway: miR-targeted genes in epithelium - TarBase;miR-targeted genes in lymphocytes - TarBase;Cell-extracellular matrix interactions;Cell junction organization;Cell-Cell communication (Consensus)

Recessive Scores

• pRec: 0.134

Intolerance Scores

• loftool: 0.0760
• rvis_EVS: -0.69
• rvis_percentile_EVS: 15.2

Haploinsufficiency Scores

• pHI: 0.864
• hipred: Y
• hipred_score: 0.825
• ghis: 0.642

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fermt2
• Phenotype: limbs/digits/tail phenotype; skeleton phenotype; embryo phenotype; respiratory system 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); 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); craniofacial phenotype; cellular phenotype; growth/size/body region phenotype

Zebrafish Information Network

• Gene name: fermt2
• Affected structure: cardiac muscle cell
• Phenotype tag: abnormal
• Phenotype quality: mislocalised

Gene ontology

• Biological process: cell-matrix adhesion;transforming growth factor beta receptor signaling pathway;integrin-mediated signaling pathway;regulation of cell shape;Wnt signaling pathway;integrin activation;cell junction assembly;substrate adhesion-dependent cell spreading;focal adhesion assembly;protein localization to membrane
• Cellular component: stress fiber;nucleus;nucleoplasm;cytoplasm;cytosol;focal adhesion;cell cortex;cell surface;extrinsic component of cytoplasmic side of plasma membrane;lamellipodium membrane;I band
• Molecular function: protein binding;phosphatidylinositol-3,4,5-trisphosphate binding;actin filament binding