ZNF141

zinc finger protein 141, the group of Zinc fingers C2H2-type|MicroRNA protein coding host genes

Basic information

Region (hg38): 4:337814-384868

Previous symbols: [ "D4S90" ]

Links

ENSG00000131127 ∙ NCBI:7700 ∙ OMIM:194648 ∙ HGNC:12926 ∙ Uniprot:Q15928 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• postaxial polydactyly type A (Supportive), mode of inheritance: AR
• polydactyly, postaxial, type A6 (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Postaxial polydactyly type A6	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	Musculoskeletal	23160277

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ZNF141 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF141 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				6	1	7
missense			14	5	10	29
nonsense						0
start loss						0
frameshift					2	2
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	14	11	14

Variants in ZNF141

This is a list of pathogenic ClinVar variants found in the ZNF141 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-343842-G-A		not specified	Uncertain significance (Mar 18, 2024)
4-343849-A-G		not specified	Uncertain significance (Nov 12, 2021)
4-343890-A-G		not specified	Uncertain significance (Jun 17, 2024)
4-344340-G-A		ZNF141-related disorder	Benign (Apr 21, 2020)
4-344401-A-C		not specified	Uncertain significance (Mar 15, 2024)
4-344402-G-A		ZNF141-related disorder	Likely benign (Sep 03, 2020)
4-344408-T-TGA		not specified • ZNF141-related disorder	Benign (Jan 02, 2020)
4-344411-G-C		ZNF141-related disorder	Benign (Aug 21, 2019)
4-344412-ATC-A		not specified • ZNF141-related disorder	Benign (Jan 06, 2020)
4-344414-C-G		not specified	Uncertain significance (Apr 01, 2024)
4-344416-T-C		ZNF141-related disorder	Benign (Apr 21, 2020)
4-358406-G-A		ZNF141-related disorder	Benign (Sep 18, 2019)
4-372673-C-T		not specified	Uncertain significance (Sep 01, 2021)
4-372790-A-G		not specified	Uncertain significance (Aug 12, 2021)
4-372799-A-G		not specified	Uncertain significance (Aug 04, 2021)
4-372807-A-G			Benign (Dec 31, 2019)
4-372823-G-A		ZNF141-related disorder	Benign (Jul 31, 2018)
4-372828-A-C		not specified	Uncertain significance (May 09, 2024)
4-372877-G-A		not specified	Uncertain significance (May 10, 2024)
4-372888-G-A		not specified	Likely benign (Mar 22, 2023)
4-372924-C-T			Likely benign (Oct 16, 2017)
4-372948-A-G		not specified	Uncertain significance (Jan 04, 2024)
4-373164-G-A		not specified	Uncertain significance (Mar 31, 2024)
4-373165-C-T		not specified	Uncertain significance (Jan 26, 2022)
4-373251-A-G		not specified	Uncertain significance (Dec 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF141	protein_coding	protein_coding	ENST00000240499	4	47051

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.104	0.784	125700	0	4	125704	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.224	232	242	0.959	0.0000116	3148
Missense in Polyphen		74	87.384	0.84683		1161
Synonymous	0.0493	85	85.6	0.993	0.00000389	816
Loss of Function	1.23	2	4.97	0.403	2.10e-7	60

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000871	0.0000871
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	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in transcriptional regulation as a repressor. Plays a role in limb development. {ECO:0000269|PubMed:23160277}.
• Pathway: Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription (Consensus)

Recessive Scores

• pRec: 0.164

Intolerance Scores

• rvis_EVS: 0.8
• rvis_percentile_EVS: 87.49

Haploinsufficiency Scores

• pHI: 0.394
• hipred: N
• hipred_score: 0.132
• ghis: 0.535

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.305

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;transcription by RNA polymerase II;anatomical structure morphogenesis;limb morphogenesis
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;metal ion binding