ZNF148

zinc finger protein 148, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 3:125225668-125375325

Links

ENSG00000163848 ∙ NCBI:7707 ∙ OMIM:601897 ∙ HGNC:12933 ∙ Uniprot:Q9UQR1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• global developmental delay, absent or hypoplastic corpus callosum, and dysmorphic facies (Strong), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Global developmental delay, absent or hypoplastic corpus callosum, and dysmorphic facies (GDACCF)	AD	Cardiovascular	The condition can involve congenital cardiac anomalies, and awareness may allow early management	Cardiovascular; Craniofacial; Musculoskeletal; Neurologic; Renal	27964749

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ZNF148 gene.

• not provided (21 variants)
• Global developmental delay, absent or hypoplastic corpus callosum, and dysmorphic facies (17 variants)
• Inborn genetic diseases (12 variants)
• ZNF148-related condition (4 variants)
• not specified (1 variants)
• Intellectual disability (1 variants)
• Autism spectrum disorder (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF148 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				3	5	8
missense		3	23	3		29
nonsense		3				3
start loss						0
frameshift	2	5	2			9
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	2	11	25	6	5

Variants in ZNF148

This is a list of pathogenic ClinVar variants found in the ZNF148 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-125232327-CT-C		Global developmental delay, absent or hypoplastic corpus callosum, and dysmorphic facies	Benign (Dec 05, 2021)
3-125232390-GCT-G		Global developmental delay, absent or hypoplastic corpus callosum, and dysmorphic facies	Likely pathogenic (Jan 11, 2017)
3-125232454-G-A			Uncertain significance (Apr 12, 2022)
3-125232607-C-A		Inborn genetic diseases	Uncertain significance (Jan 04, 2024)
3-125232674-C-T			Likely benign (Apr 16, 2018)
3-125232712-C-G		ZNF148-related disorder	Uncertain significance (Jul 18, 2023)
3-125232732-G-C		Autism spectrum disorder	Uncertain significance (-)
3-125232752-G-A			Likely benign (Dec 31, 2019)
3-125232813-G-T			Likely pathogenic (Feb 19, 2021)
3-125232848-C-T		ZNF148-related disorder	Likely benign (Aug 30, 2019)
3-125232855-T-C			Likely benign (-)
3-125232931-C-A			Uncertain significance (Apr 08, 2023)
3-125232934-T-A		Global developmental delay, absent or hypoplastic corpus callosum, and dysmorphic facies	Pathogenic (Dec 20, 2016)
3-125232963-C-T		Inborn genetic diseases	Likely benign (Feb 03, 2022)
3-125232977-C-T		Global developmental delay, absent or hypoplastic corpus callosum, and dysmorphic facies	Benign (Dec 05, 2021)
3-125233015-T-C			Uncertain significance (May 05, 2023)
3-125233027-C-T		ZNF148-related disorder	Uncertain significance (Feb 07, 2023)
3-125233059-T-G		Global developmental delay, absent or hypoplastic corpus callosum, and dysmorphic facies	Uncertain significance (Feb 03, 2020)
3-125233082-A-G			Likely benign (Dec 07, 2018)
3-125233085-ATGATCCAACAGAG-A			Uncertain significance (Apr 14, 2022)
3-125233094-CAG-C		Global developmental delay, absent or hypoplastic corpus callosum, and dysmorphic facies • Intellectual disability	Pathogenic (May 31, 2021)
3-125233102-G-A		Global developmental delay, absent or hypoplastic corpus callosum, and dysmorphic facies	Likely pathogenic (Oct 08, 2021)
3-125233142-C-CT		Global developmental delay, absent or hypoplastic corpus callosum, and dysmorphic facies	Pathogenic (Dec 20, 2016)
3-125233144-T-TG		Global developmental delay, absent or hypoplastic corpus callosum, and dysmorphic facies • Inborn genetic diseases	Likely pathogenic (Aug 23, 2017)
3-125233171-C-G			Uncertain significance (Feb 06, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF148	protein_coding	protein_coding	ENST00000360647	6	149794

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000342	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.52	213	414	0.514	0.0000208	5264
Missense in Polyphen		39	122.55	0.31822		1654
Synonymous	-0.102	153	151	1.01	0.00000787	1473
Loss of Function	4.99	0	29.0	0.00	0.00000139	407

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)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in transcriptional regulation. Represses the transcription of a number of genes including gastrin, stromelysin and enolase. Binds to the G-rich box in the enhancer region of these genes.
• Disease: DISEASE: Global developmental delay, absent or hypoplastic corpus callosum, and dysmorphic facies (GDACCF) [MIM:617260]: An autosomal dominant syndrome characterized by underdevelopment of the corpus callosum, mild to moderate developmental delay and intellectual disability, variable microcephaly or mild macrocephaly, short stature, feeding problems, facial dysmorphisms, and cardiac and renal malformations. {ECO:0000269|PubMed:27964749}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Recessive Scores

• pRec: 0.266

Intolerance Scores

• rvis_EVS: -0.54
• rvis_percentile_EVS: 20.54

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.783
• ghis: 0.659

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.702

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zfp148
• 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); normal phenotype; reproductive 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system phenotype; embryo phenotype; renal/urinary system phenotype; immune system phenotype; hearing/vestibular/ear 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); digestive/alimentary phenotype; endocrine/exocrine gland 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); growth/size/body region phenotype; cellular phenotype; homeostasis/metabolism phenotype

Zebrafish Information Network

• Gene name: znf148
• Affected structure: whole organism
• Phenotype tag: abnormal
• Phenotype quality: lethal (sensu genetics)

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;transcription by RNA polymerase II;cellular defense response;gamete generation;negative regulation of gene expression;substantia nigra development;negative regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;protein-containing complex assembly
• Cellular component: nucleus;nucleoplasm;Golgi apparatus
• Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription repressor activity, RNA polymerase II-specific;DNA-binding transcription factor activity;protein binding;sequence-specific DNA binding;transcription regulatory region DNA binding;metal ion binding