ZGRF1

protein-coding

zinc finger GRF-type containing 1, the group of Zinc fingers GRF-type|UPF1 like RNA helicases

Gene summary

The encoded protein contains GRF zinc finger (zf-GRF) and transmembrane domains. GRF zinc fingers are found in a number of DNA-binding proteins. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Apr 2017]

Previous symbols:

C4orf21

MANE transcript

NM_018392.5

Inheritance

—

ClinVar variants

U:299B:19

Top phenotype

Childhood apraxia of speech

gnomAD constraint

pLI —, LoF o/e 0.83

Max pathogenic AF

—

Genomic locus

chr4:112,539,333-112,636,995

External References & Databases

Ensembl (ENSG00000138658)

Transcript & Mutation Effects

hg38 • Region Span ~97.7 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 ZGRF1 variants in ClinVar

11 Conditions Cataloged

not specifiedTotal: 298

Childhood apraxia of speechTotal: 2

Autism spectrum disorderTotal: 2

Difficulty walkingTotal: 1

not providedTotal: 1

Progressive muscle weaknessTotal: 1

Bowel incontinenceTotal: 1

Spastic paraplegiaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_018392.5. 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			290 clinvar	19 clinvar		309
nonsense			2 clinvar			2
start loss						0
frameshift			2 clinvar			2
splice donor/acceptor (+/-2bp)			5 clinvar			5
Total	0	0	299	19	0	318

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 55 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_018392.5	RefSeq	NP_060862.3	27	MANE Select
ENST00000505019.6	Ensembl	ENSP00000424737.1	27	MANE Select
NM_001350397.2	RefSeq	NP_001337326.1	26	Standard
ENST00000309071.10	Ensembl	ENSP00000309095.5	10	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

RNA binding
zinc ion binding

Cellular Component

integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000505019
Coding exons: 27
Length: 97660
Individuals with no LoFs: 125427
Homozygous LoFs: 0
Heterozygous LoFs: 320
Defined: 125747
p: 0.00127

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.463	971	1.01e+3	0.959	0.0000480	13877
Missense (PolyPhen)		210	250.42	0.8386		3574
Synonymous	1.14	342	370	0.925	0.0000185	3871
Loss of Function	1.51	73	88.3	0.827	0.00000434	1234

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00099	0.00098	rare
Latino/Admixed American	0.0022	0.0021	notable
Ashkenazi Jewish	0.00090	0.00089	rare
East Asian	0.00091	0.00087	rare
Finnish	0.00099	0.00097	rare
European (Non-Finnish)	0.0010	0.00097	notable
South Asian	0.0022	0.0020	notable
Other	0.0020	0.0020	notable

dbNSFP Gene Annotations

Source: dbNSFP

Essentials

Essential (gene trap): N