ZNF148

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

Basic information

Region (hg38): 3:125225669-125375325

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 (55 variants)
• Inborn_genetic_diseases (47 variants)
• Global_developmental_delay,_absent_or_hypoplastic_corpus_callosum,_and_dysmorphic_facies (33 variants)
• ZNF148-related_disorder (9 variants)
• not_specified (4 variants)
• Autism_spectrum_disorder (1 variants)
• Intellectual_disability (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. These statistics are base on transcript: NM_000021964.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				10	3	13
missense		4	82	7		93
nonsense	2	5	3			10
start loss						0
frameshift	4	10	6			20
splice donor/acceptor (+/-2bp)		1	3			4
Total	6	20	94	17	3

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
		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

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

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