PDZD4

PDZ domain containing 4, the group of PDZ domain containing

Basic information

Region (hg38): X:153802165-153830565

Previous symbols: [ "PDZK4" ]

Links

ENSG00000067840

∙ NCBI:57595 ∙ OMIM:300634 ∙ HGNC:21167 ∙ Uniprot:Q76G19 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PDZD4 gene.

Inborn genetic diseases (15 variants)
Movement disorder;Coarse facial features;Microcephaly;Hyperactivity;Intellectual disability (1 variants)
Hypotonia;Autism;Hand tremor;Abnormal facial shape;Kyphoscoliosis (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PDZD4 gene is commonly pathogenic or not.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			15	1		16
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice variant						0
non coding						0
Total	0	0	16	1	0

Variants in PDZD4

This is a list of pathogenic ClinVar variants found in the PDZD4 region.

Position	Phenotype	Significance	ClinVar
X-153803412-C-T	Inborn genetic diseases	Likely benign (Oct 06, 2021)	link
X-153803473-C-G	Hand tremor;Kyphoscoliosis;Hypotonia;Autism;Abnormal facial shape	Uncertain significance (Oct 09, 2022)	link
X-153803643-G-A	Inborn genetic diseases	Uncertain significance (May 18, 2022)	link
X-153803757-C-G	Inborn genetic diseases	Uncertain significance (Mar 17, 2023)	link
X-153803869-G-C	Inborn genetic diseases	Uncertain significance (Jun 05, 2023)	link
X-153804021-G-C	Inborn genetic diseases	Uncertain significance (May 16, 2023)	link
X-153804024-G-A	Inborn genetic diseases	Uncertain significance (Jun 06, 2023)	link
X-153804030-G-A	Inborn genetic diseases	Uncertain significance (Dec 07, 2021)	link
X-153804082-G-C	Inborn genetic diseases	Uncertain significance (Dec 01, 2022)	link
X-153804153-G-A	Inborn genetic diseases	Uncertain significance (May 13, 2022)	link
X-153804158-A-C	Inborn genetic diseases	Uncertain significance (Jan 05, 2022)	link
X-153804227-C-T	Inborn genetic diseases	Uncertain significance (Mar 24, 2023)	link
X-153804327-T-C	Inborn genetic diseases	Likely benign (Apr 07, 2023)	link
X-153804332-G-C	Inborn genetic diseases	Likely benign (Apr 07, 2023)	link
X-153804555-C-T	Inborn genetic diseases	Uncertain significance (Feb 10, 2022)	link
X-153804590-C-G	Inborn genetic diseases	Uncertain significance (May 24, 2023)	link
X-153804758-G-A	Autism	Uncertain significance (-)	link
X-153804810-C-T	Inborn genetic diseases	Uncertain significance (Jul 28, 2021)	link
X-153804837-G-C	Inborn genetic diseases	Uncertain significance (Jun 22, 2021)	link
X-153805179-C-T	Inborn genetic diseases	Uncertain significance (Sep 26, 2022)	link
X-153805183-C-T	Inborn genetic diseases	Uncertain significance (Feb 28, 2023)	link
X-153806774-C-T	Inborn genetic diseases	Uncertain significance (Nov 15, 2021)	link
X-153807302-G-A	Inborn genetic diseases	Uncertain significance (Jan 18, 2023)	link
X-153807337-G-T	Inborn genetic diseases	Uncertain significance (Aug 16, 2022)	link
X-153807340-G-A	Inborn genetic diseases	Uncertain significance (Jul 14, 2021)	link

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PDZD4	protein_coding	protein_coding	ENST00000164640	8	28400

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.849	0.151	125594	4	3	125601	0.0000279

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.70	239	389	0.614	0.0000393	4985
Missense in Polyphen		70	176.36	0.39692		1991
Synonymous	0.485	165	173	0.953	0.0000179	1597
Loss of Function	3.45	3	19.4	0.155	0.00000151	310

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.000135	0.0000993
East Asian	0.0000722	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000503	0.0000352
Middle Eastern	0.0000722	0.0000544
South Asian	0.0000565	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

pRec: 0.113

Intolerance Scores

loftool: 0.121
rvis_EVS: -0.38
rvis_percentile_EVS: 27.88

Haploinsufficiency Scores

pHI: 0.468
hipred: Y
hipred_score: 0.718
ghis: 0.561

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.0335

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Pdzd4
Phenotype: normal phenotype;

Gene ontology

Biological process: protein ubiquitination
Cellular component: cell cortex
Molecular function: ubiquitin protein ligase activity