ZFPL1

protein-coding

zinc finger protein like 1

Gene summary

Predicted to enable DNA binding activity and zinc ion binding activity. Predicted to be involved in regulation of DNA-templated transcription. Located in Golgi apparatus. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_006782.4

Inheritance

—

ClinVar variants

U:58B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.39

Max pathogenic AF

—

Genomic locus

chr11:65,084,210-65,088,398

External References & Databases

Ensembl (ENSG00000162300)

Transcript & Mutation Effects

hg38 • Region Span ~4.2 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ZFPL1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 57

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_006782.4. 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						0
missense			57 clinvar	2 clinvar		59
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	58	2	0	60

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 24 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_006782.4	RefSeq	NP_006773.2	7	MANE Select
ENST00000294258.8	Ensembl	ENSP00000294258.3	7	MANE Select
ENST00000453524.6	Ensembl	ENSP00000415088.2	3	Standard
ENST00000525509.1	Ensembl	ENSP00000433673.1	1	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

regulation of transcription, DNA-templated
vesicle-mediated transport

Molecular Function

DNA binding
zinc ion binding

Cellular Component

nucleus
Golgi apparatus
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000294258
Coding exons: 7
Length: 4176
Individuals with no LoFs: 125738
Homozygous LoFs: 0
Heterozygous LoFs: 9
Defined: 125747
p: 0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.362	189	204	0.929	0.0000134	1982
Missense (PolyPhen)		58	64.806	0.89497		662
Synonymous	0.0297	86	86.4	0.996	0.00000546	685
Loss of Function	2.22	6	15.4	0.390	9.27e-7	149

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00018	0.00012	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000035	0.000035	rare
South Asian	0.000098	0.000098	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Required for cis-Golgi integrity and efficient ER to Golgi transport. Involved in the maintenance of the integrity of the cis-Golgi, possibly via its interaction with GOLGA2/GM130. {ECO:0000269|PubMed:18323775}.;

Recessive Scores

pRec: 0.0991

Intolerance Scores

LoFtool: 0.0982
RVIS EVS: 0.31
RVIS percentile EVS: 72.6

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.889

Gene Damage Prediction

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