ZFPL1

zinc finger protein like 1

Basic information

Region (hg38): 11:65084210-65088398

Links

ENSG00000162300 ∙ NCBI:7542 ∙ OMIM:619397 ∙ HGNC:12868 ∙ Uniprot:O95159 ∙ 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 ZFPL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZFPL1 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			20	1		21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	1	0

Variants in ZFPL1

This is a list of pathogenic ClinVar variants found in the ZFPL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-65084790-A-G		not specified	Uncertain significance (Jul 19, 2022)
11-65084790-A-T		not specified	Uncertain significance (Aug 02, 2022)
11-65085167-A-G		not specified	Uncertain significance (Mar 25, 2024)
11-65085173-G-A		not specified	Uncertain significance (Nov 16, 2021)
11-65085202-G-C		not specified	Uncertain significance (Oct 10, 2023)
11-65085212-G-A		not specified	Uncertain significance (May 14, 2024)
11-65086423-C-T		not specified	Uncertain significance (Dec 03, 2024)
11-65086445-G-A		not specified	Uncertain significance (Mar 01, 2024)
11-65086463-G-A		not specified	Uncertain significance (Oct 01, 2024)
11-65086469-C-T		not specified	Uncertain significance (Dec 03, 2024)
11-65086480-G-A		not specified	Uncertain significance (Jun 13, 2023)
11-65086523-C-G		not specified	Uncertain significance (Apr 25, 2022)
11-65086586-G-A		not specified	Uncertain significance (Oct 12, 2021)
11-65086592-G-T		not specified	Uncertain significance (Jul 19, 2023)
11-65086756-A-G		not specified	Uncertain significance (Oct 12, 2021)
11-65086760-C-T		not specified	Uncertain significance (Jul 09, 2024)
11-65086994-C-A		not specified	Uncertain significance (Dec 09, 2024)
11-65087015-C-T		not specified	Uncertain significance (May 30, 2023)
11-65087021-G-A		not specified	Uncertain significance (Oct 28, 2024)
11-65087054-A-G		not specified	Likely benign (May 31, 2022)
11-65087333-G-A		not specified	Uncertain significance (Mar 28, 2024)
11-65087373-A-G		not specified	Uncertain significance (Dec 15, 2021)
11-65087397-G-A		not specified	Uncertain significance (Oct 28, 2024)
11-65087400-G-A		not specified	Uncertain significance (Jan 07, 2022)
11-65087945-G-A		not specified	Uncertain significance (Jan 23, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZFPL1	protein_coding	protein_coding	ENST00000294258	7	4176

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00876	0.980	125738	0	9	125747	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.362	189	204	0.929	0.0000134	1982
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000185	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000353	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.0000980	0.0000980
Other	0.00	0.00

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.129
• hipred: N
• hipred_score: 0.423
• ghis: 0.573

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.889

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zfpl1

Gene ontology

• Biological process: regulation of transcription, DNA-templated;vesicle-mediated transport
• Cellular component: nucleus;Golgi apparatus;integral component of membrane
• Molecular function: DNA binding;zinc ion binding