ZNF550

zinc finger protein 550, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 19:57535257-57559863

Links

ENSG00000251369 ∙ NCBI:162972 ∙ ∙ HGNC:28643 ∙ Uniprot:Q7Z398 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ZNF550 gene.

• Inborn genetic diseases (22 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF550 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						0
missense						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			22			22
Total	0	0	22	0	0

Variants in ZNF550

This is a list of pathogenic ClinVar variants found in the ZNF550 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-57537212-C-G		not specified	Uncertain significance (Nov 18, 2023)
19-57537284-C-G		not specified	Uncertain significance (Nov 19, 2022)
19-57537422-T-G		not specified	Uncertain significance (Sep 16, 2021)
19-57537515-A-C		not specified	Uncertain significance (Jun 29, 2023)
19-57537542-A-T		not specified	Uncertain significance (Feb 15, 2023)
19-57537543-A-G		not specified	Uncertain significance (Nov 18, 2023)
19-57537581-A-G		not specified	Uncertain significance (Jun 27, 2022)
19-57537681-A-C		not specified	Uncertain significance (Feb 16, 2023)
19-57537750-G-A		not specified	Uncertain significance (Sep 12, 2023)
19-57537750-G-C		not specified	Uncertain significance (Jan 24, 2023)
19-57537773-A-T		not specified	Uncertain significance (Jun 06, 2023)
19-57537978-C-T		not specified	Uncertain significance (Dec 16, 2023)
19-57538028-C-T		not specified	Uncertain significance (May 10, 2024)
19-57538073-G-A		not specified	Uncertain significance (Sep 14, 2022)
19-57538130-C-T		not specified	Uncertain significance (Jun 13, 2023)
19-57538134-T-C		not specified	Uncertain significance (Dec 01, 2022)
19-57538137-G-A		not specified	Uncertain significance (May 02, 2024)
19-57538233-T-G		not specified	Uncertain significance (Jun 07, 2023)
19-57538236-A-G		not specified	Uncertain significance (Oct 26, 2022)
19-57538237-C-A		not specified	Uncertain significance (Aug 01, 2022)
19-57538254-A-T		not specified	Uncertain significance (Nov 15, 2023)
19-57538349-A-G		not specified	Uncertain significance (Mar 16, 2022)
19-57538370-C-T		not specified	Uncertain significance (Apr 14, 2022)
19-57538389-G-A		not specified	Uncertain significance (Nov 18, 2023)
19-57538455-C-T		not specified	Uncertain significance (Dec 17, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF550	protein_coding	protein_coding	ENST00000506609	2	24607

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.62e-7	0.110	125718	0	29	125747	0.000115

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0258	213	214	0.995	0.0000119	2486
Missense in Polyphen		76	81.83	0.92876		935
Synonymous	-0.954	93	82.0	1.13	0.00000430	727
Loss of Function	-0.516	9	7.48	1.20	3.87e-7	89

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000185	0.000185
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000123	0.000123
Middle Eastern	0.00	0.00
South Asian	0.000294	0.000294
Other	0.000489	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in transcriptional regulation.
• Pathway: Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription (Consensus)

Intolerance Scores

• loftool: 0.686
• rvis_EVS: 0.64
• rvis_percentile_EVS: 84.05

Haploinsufficiency Scores

• pHI: 0.133
• hipred: N
• hipred_score: 0.112
• ghis: 0.474

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Gene ontology

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