ZNF407

zinc finger protein 407, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 18:74597869-75065671

Links

ENSG00000215421 ∙ NCBI:55628 ∙ OMIM:615894 ∙ HGNC:19904 ∙ Uniprot:Q9C0G0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• intellectual disability (Limited), mode of inheritance: AD
• complex neurodevelopmental disorder (Limited), mode of inheritance: AR
• short stature, impaired intellectual development, microcephaly, hypotonia, and ocular anomalies (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Short stature, impaired intellectual development, microcephaly, hypotonia, and ocular anomalies	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Craniofacial; Musculoskeletal; Neurologic; Ophthalmologic	24907849; 32737394

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ZNF407 gene.

• Inborn genetic diseases (113 variants)
• not provided (102 variants)
• not specified (77 variants)
• See cases (4 variants)
• Short stature, impaired intellectual development, microcephaly, hypotonia, and ocular anomalies (2 variants)
• ZNF407-related condition (1 variants)
• Radioulnar synostosis-microcephaly-scoliosis syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF407 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			15	33	17	65
missense			152	22	10	184
nonsense						0
start loss						0
frameshift			1			1
inframe indel			1			1
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding			3	1		4
Total	0	0	172	56	27

Variants in ZNF407

This is a list of pathogenic ClinVar variants found in the ZNF407 region.

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

Position	Type	Phenotype	Significance	ClinVar
18-74631052-T-C		not specified	Likely benign (-)
18-74631060-A-G		See cases	Uncertain significance (Jul 10, 2020)
18-74631089-A-G		not specified	Uncertain significance (Dec 19, 2022)
18-74631100-A-T			Likely benign (May 03, 2018)
18-74631105-A-G		not specified	Uncertain significance (Aug 14, 2023)
18-74631113-G-T		not specified	Uncertain significance (Aug 18, 2015)
18-74631115-C-T		ZNF407-related disorder	Likely benign (Aug 29, 2019)
18-74631116-G-A		not specified	Uncertain significance (Nov 21, 2023)
18-74631194-T-C		not specified	Uncertain significance (Mar 20, 2023)
18-74631195-C-G		not specified	Uncertain significance (Dec 04, 2023)
18-74631200-A-G		not specified • ZNF407-related disorder	Benign (Apr 10, 2019)
18-74631203-G-T		not specified	Uncertain significance (Jul 25, 2023)
18-74631225-A-G		not specified • ZNF407-related disorder	Benign (Mar 05, 2019)
18-74631231-A-T		not specified	Uncertain significance (Dec 08, 2023)
18-74631265-G-A		not specified • ZNF407-related disorder	Likely benign (Apr 07, 2021)
18-74631285-A-G		not specified	Uncertain significance (Nov 21, 2023)
18-74631329-G-C		not specified	Uncertain significance (Nov 07, 2022)
18-74631336-T-A		ZNF407-related disorder	Likely benign (Jun 29, 2021)
18-74631344-G-C			Uncertain significance (Oct 18, 2022)
18-74631410-C-G		not specified	Conflicting classifications of pathogenicity (Apr 04, 2023)
18-74631437-A-G		not specified	Likely benign (May 08, 2023)
18-74631446-G-T		not specified • ZNF407-related disorder	Benign/Likely benign (Oct 01, 2022)
18-74631509-A-G		not specified	Benign/Likely benign (Jun 06, 2018)
18-74631634-T-C		not specified	Likely benign (Jun 27, 2016)
18-74631683-C-T			Uncertain significance (Aug 16, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF407	protein_coding	protein_coding	ENST00000299687	8	512522

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	3.79e-10	124632	0	7	124639	0.0000281

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.859	1173	1.26e+3	0.932	0.0000719	14831
Missense in Polyphen		280	426.68	0.65623		4848
Synonymous	-2.20	565	502	1.13	0.0000329	4285
Loss of Function	7.44	2	68.4	0.0293	0.00000360	960

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000581	0.0000581
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000467	0.0000464
European (Non-Finnish)	0.0000354	0.0000354
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in transcriptional regulation.

Intolerance Scores

• loftool: 0.0482
• rvis_EVS: -0.94
• rvis_percentile_EVS: 9.38

Haploinsufficiency Scores

• pHI: 0.165
• hipred: N
• hipred_score: 0.334
• ghis: 0.543

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.634

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zfp407

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;regulation of gene expression
• Cellular component: nucleus;histone methyltransferase complex
• Molecular function: RNA polymerase II core promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;zinc ion binding