ZNF541

zinc finger protein 541, the group of Zinc fingers C2H2-type|Myb/SANT domain containing

Basic information

Region (hg38): 19:47520689-47573148

Links

ENSG00000118156 ∙ NCBI:84215 ∙ OMIM:619942 ∙ HGNC:25294 ∙ Uniprot:Q9H0D2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• male infertility with azoospermia or oligozoospermia due to single gene mutation (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ZNF541 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF541 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				2		2
missense						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	0	2	0

Variants in ZNF541

This is a list of pathogenic ClinVar variants found in the ZNF541 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-47540323-G-A			Likely benign (Oct 01, 2022)
19-47544921-C-T			Uncertain significance (-)
19-47545853-G-A			Likely benign (Oct 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF541	protein_coding	protein_coding	ENST00000314121	15	35172

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.00000180	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.64	534	736	0.726	0.0000452	8798
Missense in Polyphen		108	203.9	0.52968		2516
Synonymous	1.50	294	328	0.895	0.0000227	2820
Loss of Function	6.17	3	50.1	0.0598	0.00000289	603

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: Component of some chromatin remodeling multiprotein complex that plays a role during spermatogenesis. {ECO:0000250|UniProtKB:Q0GGX2}.

Intolerance Scores

• rvis_EVS: 1.02
• rvis_percentile_EVS: 90.92

Haploinsufficiency Scores

• pHI: 0.227

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.216

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zfp541

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;multicellular organism development;spermatogenesis;cell differentiation
• Cellular component: histone deacetylase complex;nucleus;transcription factor complex
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription factor activity;transcription factor binding;transcription regulatory region DNA binding;metal ion binding