ZNF91

protein-coding

zinc finger protein 91, the group of Zinc fingers C2H2-type

Gene summary

The ZNF91 gene encodes a zinc finger protein of the KRAB (Kruppel-associated box) subfamily (Bellefroid et al., 1991, 1993 [PubMed 2023909] [PubMed 8467795]).[supplied by OMIM, May 2010]

MANE transcript

NM_003430.4

Inheritance

—

ClinVar variants

U:172B:12

Top phenotype

Congenital nephrotic syndrome

gnomAD constraint

pLI —, LoF o/e 0.18

Max pathogenic AF

—

Genomic locus

chr19:23,304,991-23,395,471

External References & Databases

Ensembl (ENSG00000167232)

Transcript & Mutation Effects

hg38 • Region Span ~90.5 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 ZNF91 variants in ClinVar

8 Conditions Cataloged

not specifiedTotal: 174

not providedTotal: 7

Congenital nephrotic syndromeTotal: 1

EBV-positive nodal T- and NK-cell lymphomaTotal: 1

CataractTotal: 1

Retinal dystrophyTotal: 1

MicrocephalyTotal: 1

MicrophthalmiaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_003430.4. 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				4 clinvar	1 clinvar	5
missense			171 clinvar	6 clinvar	1 clinvar	178
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	172	10	2	184

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 35 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_003430.4	RefSeq	NP_003421.2	4	MANE Select
ENST00000300619.12	Ensembl	ENSP00000300619.6	4	MANE Select
NM_001300951.2	RefSeq	NP_001287880.1	3	Standard
ENST00000397082.2	Ensembl	ENSP00000380272.2	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

regulation of transcription by RNA polymerase II
negative regulation of transcription, DNA-templated
negative regulation of transposon integration

Molecular Function

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

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000300619
Coding exons: 4
Length: 90570
Individuals with no LoFs: 119731
Homozygous LoFs: 0
Heterozygous LoFs: 2
Defined: 119733
p: 0.00000835

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.555	627	589	1.06	0.0000270	7819
Missense (PolyPhen)		244	233.2	1.0463		3172
Synonymous	-2.09	241	203	1.19	0.00000957	2079
Loss of Function	1.76	1	5.44	0.184	2.30e-7	66

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000032	0.000032	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.0000091	0.0000091	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Transcription factor specifically required to repress SINE-VNTR-Alu (SVA) retrotransposons: recognizes and binds SVA sequences and represses their expression by recruiting a repressive complex containing TRIM28/KAP1 (PubMed:25274305). May also bind the promoter of the FCGR2B gene, leading to repress its expression; however, additional evidences are required to confirm this result in vivo (PubMed:11470777). {ECO:0000269|PubMed:25274305, ECO:0000305|PubMed:11470777}.;

Intolerance Scores

LoFtool: 0.716
RVIS EVS: 2.14
RVIS percentile EVS: 97.97

Essentials

Essential (CRISPR): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.125

Gene Damage Prediction

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