NHERF2

NHERF family PDZ scaffold protein 2, the group of NHERF family PDZ scaffold proteins|PDZ domain containing

Basic information

Region (hg38): 16:2025355-2039026

Previous symbols: [ "SLC9A3R2" ]

Links

ENSG00000065054 ∙ NCBI:9351 ∙ OMIM:606553 ∙ HGNC:11076 ∙ Uniprot:Q15599 ∙ 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 NHERF2 gene.

• Inborn genetic diseases (11 variants)
• not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NHERF2 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			10	3	2	15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	3	2

Variants in NHERF2

This is a list of pathogenic ClinVar variants found in the NHERF2 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-2027043-G-T		not specified	Uncertain significance (Apr 07, 2023)
16-2027059-G-T		not specified	Uncertain significance (May 18, 2023)
16-2027088-A-G		not specified	Uncertain significance (Feb 16, 2023)
16-2027089-G-C			Benign (Dec 31, 2019)
16-2027205-A-G		not specified	Uncertain significance (Mar 23, 2023)
16-2029618-C-T		not specified	Uncertain significance (Jan 24, 2024)
16-2029619-G-A		not specified	Uncertain significance (May 11, 2022)
16-2029620-G-A			Uncertain significance (-)
16-2029681-G-A		not specified	Uncertain significance (Nov 08, 2022)
16-2029697-G-A		not specified	Uncertain significance (Oct 05, 2023)
16-2029711-G-C		not specified	Uncertain significance (Jul 06, 2021)
16-2029725-G-C		not specified	Uncertain significance (Jan 04, 2024)
16-2029730-C-T		not specified	Uncertain significance (Oct 27, 2023)
16-2036330-A-G		not specified	Uncertain significance (Sep 13, 2023)
16-2036373-G-A		not specified	Uncertain significance (Nov 08, 2022)
16-2036395-G-A			Uncertain significance (-)
16-2036420-C-T			Likely benign (Jan 01, 2023)
16-2036421-G-C		not specified	Uncertain significance (Jun 22, 2021)
16-2036437-C-G		not specified	Uncertain significance (Oct 26, 2022)
16-2036439-G-A		not specified	Uncertain significance (Nov 21, 2022)
16-2036451-C-T		not specified	Likely benign (Jan 25, 2023)
16-2036465-G-A		not specified	Uncertain significance (Nov 09, 2021)
16-2036468-C-T			Likely benign (Feb 01, 2023)
16-2036480-C-G		not specified	Uncertain significance (Aug 08, 2022)
16-2036483-G-A		not specified	Uncertain significance (Nov 16, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NHERF2	protein_coding	protein_coding	ENST00000424542	7	13671

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0384	0.955	124167	0	5	124172	0.0000201

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.174	209	202	1.03	0.0000138	2111
Missense in Polyphen		70	79.388	0.88175		898
Synonymous	-0.950	96	84.9	1.13	0.00000592	691
Loss of Function	2.39	5	15.0	0.333	8.94e-7	158

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000682	0.0000650
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000560	0.0000557
Finnish	0.00	0.00
European (Non-Finnish)	0.0000279	0.0000267
Middle Eastern	0.0000560	0.0000557
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Scaffold protein that connects plasma membrane proteins with members of the ezrin/moesin/radixin family and thereby helps to link them to the actin cytoskeleton and to regulate their surface expression. Necessary for cAMP-mediated phosphorylation and inhibition of SLC9A3 (PubMed:18829453). May also act as scaffold protein in the nucleus. {ECO:0000269|PubMed:10455146, ECO:0000269|PubMed:18829453, ECO:0000269|PubMed:9096337}.
• Pathway: Aldosterone-regulated sodium reabsorption - Homo sapiens (human);Beta-agonist/Beta-blocker Pathway, Pharmacodynamics;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;LPA receptor mediated events;PDGFR-beta signaling pathway (Consensus)

Recessive Scores

• pRec: 0.237

Intolerance Scores

• loftool: 0.769
• rvis_EVS: 0.44
• rvis_percentile_EVS: 77.85

Haploinsufficiency Scores

• pHI: 0.195
• hipred: Y
• hipred_score: 0.629
• ghis: 0.447

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.491

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Slc9a3r2
• Phenotype: homeostasis/metabolism phenotype

Gene ontology

• Biological process: protein-containing complex assembly
• Cellular component: nucleus;plasma membrane;focal adhesion;endomembrane system;apical plasma membrane;extracellular exosome
• Molecular function: signaling receptor binding;protein binding;beta-catenin binding;protein C-terminus binding;phosphatase binding;protein-containing complex scaffold activity;cadherin binding