ZNF713

protein-coding

zinc finger protein 713, the group of Zinc fingers C2H2-type

Gene summary

The protein encoded by this gene contains C2H2 zinc finger domains. In some individuals, a CGG-repeat expansion from 5-22 repeats to 68-450 repeats has been identified in the first intron of this gene. This mutation is thought to effect the expression of this gene and it has been proposed that it may be associated with Autistic Spectrum Disorder. [provided by RefSeq, Jul 2016]

MANE transcript

NM_182633.3

Inheritance

ClinVar variants

U:41B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.63

Max pathogenic AF

—

Genomic locus

chr7:55,887,456-55,942,530

External References & Databases

Ensembl (ENSG00000178665)

Transcript & Mutation Effects

hg38 • Region Span ~55.1 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

autismLIMITED

Inheritance Pattern: AD

Disease ID:MONDO:0005260

Submitter: G2P

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ZNF713 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 43

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_182633.3. 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				1 clinvar		1
missense			41 clinvar	2 clinvar		43
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	41	3	0	44

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 11 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_182633.3	RefSeq	NP_872439.2	4	MANE Select
ENST00000429591.4	Ensembl	ENSP00000416662.3	4	MANE Select
NM_001366796.2	RefSeq	NP_001353725.1	4	Standard
ENST00000411863.2	Ensembl	ENSP00000416974.2	2	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

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: ENST00000429591
Coding exons: 4
Length: 54750
Individuals with no LoFs: 125689
Homozygous LoFs: 0
Heterozygous LoFs: 58
Defined: 125747
p: 0.000231

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.01	188	231	0.813	0.0000114	2886
Missense (PolyPhen)		73	76.392	0.95559		903
Synonymous	1.25	67	81.3	0.824	0.00000428	735
Loss of Function	1.44	11	17.5	0.629	8.00e-7	231

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.00012	0.00012	rare
Ashkenazi Jewish	0.00050	0.00050	rare
East Asian	0.00044	0.00044	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00023	0.00023	rare
South Asian	0.00042	0.00042	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May be involved in transcriptional regulation.;
Disease: DISEASE: Note=A 7p11.2 folate-sensitive fragile site, FRA7A, has been identified in 2 unrelated families diagnosed with an autistic disorder. FRA7A is associated with a CGG-repeat expansion in a ZNF713 5'-intron. In the first family, the expanded allele contained about 450 CGG-repeats. It showed hypermethylation and reduced ZNF713 expression. In the second family, 3 autistic siblings exhibited a heterozygous expansion of about 70 repeats, corresponding to premutations, which were partially or mosaically methylated. Mitotic instability of the premutation was observed in one affected sibling. In this family, ZNF713 tends to be up- regulated. It has been suggested that ZNF713 misregulation in the brain might be involved in the pathogenicity of autistic disorder (PubMed:25196122). {ECO:0000269|PubMed:25196122}.;

Intolerance Scores

RVIS EVS: -0.85
RVIS percentile EVS: 11.06

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.117

Gene Damage Prediction

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