ZNF141

protein-coding

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

Gene summary

The protein encoded by this gene is a zinc finger protein that may be a tumor suppressor. Defects in this gene have been associated with autosomal recessive postaxial polydactyly type A. [provided by RefSeq, Jan 2017]

Previous symbols:

D4S90

MANE transcript

NM_003441.4

Inheritance

ClinVar variants

P:1U:54B:28

Top phenotype

Postaxial polydactyly type A6

gnomAD constraint

pLI —, LoF o/e 0.4

Max pathogenic AF

—

Genomic locus

chr4:337,814-384,868

External References & Databases

Ensembl (ENSG00000131127)

Transcript & Mutation Effects

hg38 • Region Span ~47.1 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

postaxial polydactyly type ASUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0019673

Submitter: Orphanet

polydactyly, postaxial, type A6LIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0014090

Submitter: PanelApp Australia

polydactyly, postaxial, type A6LIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0014090

Submitter: Labcorp Genetics (formerly Invitae)

Clinical Genomic Database (CGD)

Postaxial polydactyly type A6AR

Manifestation: Musculoskeletal

Intervention: General

Rationale: 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

Refs: 23160277

Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ZNF141 variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 71

ZNF141-related disorderTotal: 20

not providedTotal: 8

Polydactyly, postaxial, type A6Total: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_003441.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				6 clinvar	1 clinvar	7
missense		1 clinvar	54 clinvar	14 clinvar	5 clinvar	74
nonsense						0
start loss						0
frameshift				2 clinvar		2
splice donor/acceptor (+/-2bp)						0
Total	0	1	54	22	6	83

Highest pathogenic variant AF is 0.0000013832847

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 27 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_003441.4	RefSeq	NP_003432.1	4	MANE Select
ENST00000240499.8	Ensembl	ENSP00000240499.7	4	MANE Select
NM_001348277.2	RefSeq	NP_001335206.1	1	Standard
NM_001348278.2	RefSeq	NP_001335207.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Gene expression (Transcription)
Generic Transcription Pathway
RNA Polymerase II Transcription

Biological Process

regulation of transcription by RNA polymerase II
transcription by RNA polymerase II
anatomical structure morphogenesis
limb morphogenesis

Molecular Function

DNA-binding transcription factor activity, RNA polymerase II-specific
DNA binding
metal ion binding

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000240499
Coding exons: 4
Length: 47051
Individuals with no LoFs: 125700
Homozygous LoFs: 0
Heterozygous LoFs: 4
Defined: 125704
p: 0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.224	232	242	0.959	0.0000116	3148
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000087	0.000087	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May be involved in transcriptional regulation as a repressor. Plays a role in limb development. {ECO:0000269|PubMed:23160277}.;

Recessive Scores

pRec: 0.164

Intolerance Scores

RVIS EVS: 0.8
RVIS percentile EVS: 87.49

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.305

Gene Damage Prediction

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