CHRFAM7A

CHRNA7 (exons 5-10) and FAM7A (exons A-E) fusion

Basic information

Region (hg38): 15:30360566-30393849

Links

ENSG00000166664 ∙ NCBI:89832 ∙ OMIM:609756 ∙ HGNC:15781 ∙ Uniprot:Q494W8 ∙ AlphaFold ∙ 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 CHRFAM7A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CHRFAM7A 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				1		1
missense			19	1		20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	2	0

Variants in CHRFAM7A

This is a list of pathogenic ClinVar variants found in the CHRFAM7A region.

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

Position	Type	Phenotype	Significance	ClinVar
15-30362336-G-A		not specified	Likely benign (Apr 22, 2022)
15-30362448-C-T		not specified	Uncertain significance (May 11, 2022)
15-30362558-G-A		not specified	Uncertain significance (Feb 15, 2023)
15-30362661-T-C		not specified	Uncertain significance (Apr 25, 2022)
15-30362774-A-C		not specified	Uncertain significance (Nov 20, 2024)
15-30367435-C-T		not specified	Uncertain significance (Feb 23, 2023)
15-30367473-A-G		not specified	Uncertain significance (May 14, 2024)
15-30367476-G-A		not specified	Uncertain significance (Oct 29, 2024)
15-30371117-G-A			Likely benign (Apr 01, 2025)
15-30371133-A-G		not specified	Uncertain significance (Jul 19, 2022)
15-30371170-G-A		not specified	Uncertain significance (Oct 05, 2021)
15-30371172-A-G		not specified	Uncertain significance (Jun 09, 2022)
15-30372165-C-T		not specified	Uncertain significance (Dec 04, 2024)
15-30372170-T-C		not specified	Uncertain significance (Apr 08, 2024)
15-30372197-G-A		not specified	Uncertain significance (Nov 09, 2024)
15-30372208-G-C		not specified	Uncertain significance (Aug 02, 2023)
15-30372286-A-G			Likely benign (Jul 15, 2018)
15-30372326-C-G		not specified	Uncertain significance (Nov 13, 2023)
15-30372989-C-G		not specified	Uncertain significance (Aug 12, 2021)
15-30373016-A-G		not specified	Uncertain significance (Nov 10, 2024)
15-30373056-C-T		not specified	Uncertain significance (Dec 04, 2024)
15-30373137-T-C		not specified	Uncertain significance (Feb 16, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CHRFAM7A	protein_coding	protein_coding	ENST00000299847	8	32610

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000232	0.769	44386	13735	67074	125195	0.405

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.585	108	127	0.854	0.00000733	2635
Missense in Polyphen		59	70.535	0.83646		1176
Synonymous	0.722	46	52.7	0.873	0.00000344	765
Loss of Function	1.06	7	10.7	0.651	4.57e-7	200

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.649	0.647
Ashkenazi Jewish	0.353	0.349
East Asian	0.672	0.736
Finnish	0.364	0.384
European (Non-Finnish)	0.357	0.373
Middle Eastern	0.672	0.736
South Asian	0.461	0.458
Other	0.406	0.427

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• pHI: 0.0977

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.137

Gene Damage Prediction

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

Gene ontology

• Biological process: signal transduction;chemical synaptic transmission;synaptic transmission, cholinergic;ion transmembrane transport;regulation of membrane potential;nervous system process
• Cellular component: integral component of plasma membrane;acetylcholine-gated channel complex;neuron projection;synapse
• Molecular function: extracellular ligand-gated ion channel activity;acetylcholine receptor activity;acetylcholine binding