ATF7-NPFF

protein-coding

ATF7-NPFF readthrough

Gene summary

Predicted to enable DNA binding activity; DNA-binding transcription factor activity; and zinc ion binding activity. Predicted to be involved in DNA-templated transcription and regulation of DNA-templated transcription. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

N/A

Inheritance

—

ClinVar variants

U:2B:2

Top phenotype

Inborn genetic diseases

gnomAD constraint

pLI —, LoF o/e 0.16

Max pathogenic AF

—

Genomic locus

chr12:53,506,691-53,625,979

External References & Databases

Ensembl (ENSG00000267281)

NCBI Gene (114108587)

Transcript & Mutation Effects

hg38 • Region Span ~119.3 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 ATF7-NPFF variants in ClinVar

2 Conditions Cataloged

Inborn genetic diseasesTotal: 7

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

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

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 3 of 3 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001366559.1	RefSeq	NP_001353488.1	12	Standard
NM_001366560.1	RefSeq	NP_001353489.1	12	Standard
ENST00000591834.1	Ensembl	ENSP00000466174.1	12	Standard

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000591834
Coding exons: 12
Length: 119292
Individuals with no LoFs: 125736
Homozygous LoFs: 0
Heterozygous LoFs: 3
Defined: 125739
p: 0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.06	172	267	0.645	0.0000143	2958
Missense (PolyPhen)		46	98.862	0.46529		1004
Synonymous	1.56	75	94.3	0.795	0.00000452	986
Loss of Function	3.85	4	24.6	0.162	0.00000147	256

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000063	0.000062	rare
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent