ATF7-NPFF

ATF7-NPFF readthrough

Basic information

Region (hg38): 12:53506690-53625979

Links

ENSG00000267281 ∙ NCBI:114108587 ∙ ∙ HGNC:55073 ∙ ∙ ∙ 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 ATF7-NPFF gene.

• Inborn genetic diseases (7 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATF7-NPFF 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					2	2
missense			1			1
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region						0
non coding			2	2		4
Total	0	0	4	2	2

Variants in ATF7-NPFF

This is a list of pathogenic ClinVar variants found in the ATF7-NPFF region.

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

Position	Type	Phenotype	Significance	ClinVar
12-53506801-G-A		not specified	Uncertain significance (Jul 09, 2021)
12-53506856-A-G			Benign (Dec 31, 2019)
12-53506882-T-C			Benign (Dec 31, 2019)
12-53506891-A-G		not specified	Uncertain significance (Apr 12, 2022)
12-53507051-C-T		not specified	Uncertain significance (Mar 01, 2024)
12-53507136-C-G		not specified	Uncertain significance (Sep 14, 2022)
12-53507423-C-T		not specified	Likely benign (May 16, 2022)
12-53507426-C-A		not specified	Uncertain significance (Sep 06, 2022)
12-53507461-T-C		not specified	Likely benign (Mar 23, 2022)
12-53507464-C-G		not specified	Uncertain significance (Dec 06, 2021)
12-53524654-T-C			Benign (Jul 06, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ATF7-NPFF	protein_coding	protein_coding	ENST00000591834	12	119292

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.884	0.116	125736	0	3	125739	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.06	172	267	0.645	0.0000143	2958
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000916	0.0000906
Ashkenazi Jewish	0.0000994	0.0000992
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP