NHERF4

NHERF family PDZ scaffold protein 4, the group of PDZ domain containing|NHERF family PDZ scaffold proteins

Basic information

Region (hg38): 11:119185457-119190223

Previous symbols: [ "PDZK2", "PDZD3" ]

Links

ENSG00000172367 ∙ NCBI:79849 ∙ OMIM:607146 ∙ HGNC:19891 ∙ Uniprot:Q86UT5 ∙ 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 NHERF4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NHERF4 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			43	3		46
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	43	3	0

Variants in NHERF4

This is a list of pathogenic ClinVar variants found in the NHERF4 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-119185507-G-A		not specified	Likely benign (Jun 16, 2023)
11-119185940-C-T		not specified	Uncertain significance (Mar 19, 2024)
11-119185943-C-T		not specified	Uncertain significance (Jun 02, 2023)
11-119186496-C-T		not specified	Uncertain significance (Nov 10, 2022)
11-119186497-G-A		not specified	Uncertain significance (Dec 20, 2023)
11-119186518-G-C		not specified	Uncertain significance (Sep 27, 2024)
11-119186526-G-A		not specified	Likely benign (Feb 06, 2024)
11-119186561-G-C		not specified	Uncertain significance (Feb 27, 2024)
11-119186563-T-C		not specified	Uncertain significance (Feb 07, 2023)
11-119186623-G-C		not specified	Uncertain significance (Sep 02, 2024)
11-119186688-G-A		not specified	Uncertain significance (Mar 24, 2023)
11-119187276-C-T		not specified	Uncertain significance (Jan 08, 2025)
11-119187277-G-A		not specified	Uncertain significance (Mar 07, 2023)
11-119187285-C-T		not specified	Uncertain significance (Feb 08, 2025)
11-119187346-G-A		not specified	Uncertain significance (Feb 28, 2023)
11-119187353-G-T		not specified	Uncertain significance (Jan 19, 2022)
11-119187362-A-C		not specified	Uncertain significance (Jun 10, 2024)
11-119187367-C-T		not specified	Uncertain significance (Feb 12, 2025)
11-119187372-C-T		not specified	Uncertain significance (Jan 06, 2023)
11-119187391-C-T		not specified	Uncertain significance (May 24, 2024)
11-119187417-A-C		not specified	Uncertain significance (Apr 17, 2024)
11-119187417-A-G		not specified	Likely benign (Feb 08, 2025)
11-119187436-G-T		not specified	Uncertain significance (Aug 12, 2024)
11-119187635-G-T		not specified	Uncertain significance (Dec 16, 2024)
11-119187638-C-T		not specified	Uncertain significance (Jan 31, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NHERF4	protein_coding	protein_coding	ENST00000355547	11	4767

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.35e-12	0.0950	125569	0	179	125748	0.000712

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.422	271	291	0.930	0.0000175	3163
Missense in Polyphen		77	91.594	0.84067		989
Synonymous	0.879	109	121	0.898	0.00000689	1103
Loss of Function	0.570	20	22.9	0.872	0.00000125	257

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000410	0.000410
Ashkenazi Jewish	0.00	0.00
East Asian	0.00174	0.00174
Finnish	0.000139	0.000139
European (Non-Finnish)	0.00102	0.00102
Middle Eastern	0.00174	0.00174
South Asian	0.000270	0.000261
Other	0.00115	0.00114

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a regulatory protein that associates with GUCY2C and negatively modulates its heat-stable enterotoxin-mediated activation (PubMed:11950846). Stimulates SLC9A3 activity in the presence of elevated calcium ions (PubMed:19088451). {ECO:0000269|PubMed:11950846, ECO:0000269|PubMed:19088451}.
• Pathway: Disease;Intestinal infectious diseases;Uptake and actions of bacterial toxins;Infectious disease (Consensus)

Recessive Scores

• pRec: 0.128

Intolerance Scores

• loftool: 0.983
• rvis_EVS: -0.04
• rvis_percentile_EVS: 50.45

Haploinsufficiency Scores

• pHI: 0.140
• hipred: N
• hipred_score: 0.144
• ghis: 0.424

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.715

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pdzd3
• Phenotype: homeostasis/metabolism phenotype

Gene ontology

• Biological process: ion transport;water transport;receptor guanylyl cyclase signaling pathway;response to toxic substance;negative regulation of cGMP-mediated signaling;negative regulation of guanylate cyclase activity
• Cellular component: cytosol;brush border;subapical complex;apical part of cell
• Molecular function: protein binding;protein C-terminus binding;ion channel inhibitor activity;guanylate cyclase inhibitor activity;ubiquitin-specific protease binding