ZNF644

zinc finger protein 644, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 1:90915297-91022272

Links

ENSG00000122482 ∙ NCBI:84146 ∙ OMIM:614159 ∙ HGNC:29222 ∙ Uniprot:Q9H582 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• myopia 21, autosomal dominant (Limited), mode of inheritance: AD
• myopia 21, autosomal dominant (Limited), mode of inheritance: AD
• myopia 21, autosomal dominant (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Myopia 21, autosomal dominant	AD	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	Ophthalmologic	21695231

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ZNF644 gene.

• Inborn genetic diseases (53 variants)
• not provided (21 variants)
• Myopia 21, autosomal dominant (4 variants)
• ZNF644-related condition (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF644 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				5	4	9
missense			56	5	4	65
nonsense			1			1
start loss			1			1
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	59	10	8

Variants in ZNF644

This is a list of pathogenic ClinVar variants found in the ZNF644 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-90916206-C-T		Myopia 21, autosomal dominant	Pathogenic (Jun 01, 2011)
1-90916835-G-A			Uncertain significance (Aug 26, 2022)
1-90916849-G-A			Benign (May 18, 2018)
1-90916850-G-A		not specified	Uncertain significance (Nov 22, 2023)
1-90916898-C-T		ZNF644-related disorder	Benign (Jul 31, 2019)
1-90916902-G-C		not specified	Uncertain significance (Dec 11, 2023)
1-90916920-T-C			Uncertain significance (-)
1-90916929-G-C		not specified	Uncertain significance (Jul 06, 2021)
1-90918075-G-A			Likely benign (Jan 01, 2023)
1-90918109-T-C		not specified	Uncertain significance (Dec 20, 2021)
1-90937490-T-C		Myopia 21, autosomal dominant	Uncertain significance (Jan 07, 2020)
1-90937494-T-C		not specified	Uncertain significance (Dec 27, 2023)
1-90937498-C-G			Uncertain significance (Mar 15, 2023)
1-90937587-G-C		not specified	Uncertain significance (Sep 28, 2022)
1-90937668-G-C		not specified	Uncertain significance (Nov 07, 2022)
1-90937673-T-G		not specified	Uncertain significance (Aug 22, 2023)
1-90937678-CT-C		Myopia 21, autosomal dominant	Uncertain significance (Apr 05, 2018)
1-90937700-G-T		not specified	Uncertain significance (Mar 16, 2022)
1-90937773-T-C		not specified	Uncertain significance (Dec 16, 2023)
1-90937811-T-C		not specified	Uncertain significance (Mar 21, 2022)
1-90937849-A-G		ZNF644-related disorder	Benign (Jan 02, 2020)
1-90937874-C-T			Likely benign (Feb 01, 2024)
1-90937878-G-A		not specified	Uncertain significance (Oct 25, 2022)
1-90937883-T-C		ZNF644-related disorder • not specified	Conflicting classifications of pathogenicity (Jul 11, 2023)
1-90937941-C-T		not specified	Uncertain significance (Dec 21, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF644	protein_coding	protein_coding	ENST00000370440	5	106971

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.000860	125727	0	16	125743	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.55	548	660	0.830	0.0000341	8774
Missense in Polyphen		165	270.63	0.6097		3551
Synonymous	-0.303	247	241	1.02	0.0000127	2455
Loss of Function	5.53	6	46.9	0.128	0.00000282	683

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000223	0.000223
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.0000545	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000265	0.0000264
Middle Eastern	0.0000545	0.0000544
South Asian	0.0000980	0.0000980
Other	0.000329	0.000326

dbNSFP

Source: dbNSFP

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

Recessive Scores

• pRec: 0.103

Intolerance Scores

• loftool: 0.238
• rvis_EVS: -0.32
• rvis_percentile_EVS: 30.94

Haploinsufficiency Scores

• pHI: 0.534
• hipred: N
• hipred_score: 0.435
• ghis: 0.693

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.908

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zfp644

Zebrafish Information Network

• Gene name: znf644b
• Affected structure: retina
• Phenotype tag: abnormal
• Phenotype quality: increased occurrence

Gene ontology

• Biological process: regulation of transcription, DNA-templated;regulation of transcription by RNA polymerase II
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;DNA-binding transcription factor activity;metal ion binding