AMPH

amphiphysin, the group of N-BAR domain containing

Basic information

Region (hg38): 7:38383703-38631420

Links

ENSG00000078053 ∙ NCBI:273 ∙ OMIM:600418 ∙ HGNC:471 ∙ Uniprot:P49418 ∙ 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 AMPH gene.

• Inborn genetic diseases (19 variants)
• not provided (12 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the AMPH 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				5		5
missense			17	5	2	24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				2		2
Total	0	0	17	12	2

Variants in AMPH

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

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

Position	Type	Phenotype	Significance	ClinVar
7-38391842-T-C		not specified	Uncertain significance (Jan 22, 2024)
7-38391869-G-A			Likely benign (Aug 10, 2018)
7-38391916-C-G		not specified	Likely benign (Jul 12, 2022)
7-38391924-T-A		not specified	Uncertain significance (Jan 26, 2023)
7-38391954-C-T		not specified	Uncertain significance (Oct 30, 2023)
7-38391990-C-G		not specified	Uncertain significance (Feb 08, 2023)
7-38392001-G-A		not specified	Uncertain significance (May 11, 2022)
7-38394033-G-C		not specified	Uncertain significance (Nov 02, 2023)
7-38394068-T-G		not specified	Uncertain significance (Dec 13, 2022)
7-38394131-C-T			Likely benign (Jul 11, 2018)
7-38394163-C-A			Benign (Jun 14, 2018)
7-38417853-C-T		not specified	Likely benign (Jan 26, 2022)
7-38417854-G-A		not specified	Uncertain significance (Aug 04, 2023)
7-38417857-T-C		not specified	Uncertain significance (Mar 29, 2022)
7-38417881-C-T		not specified	Uncertain significance (Sep 25, 2023)
7-38426961-A-G		not specified	Uncertain significance (Mar 01, 2024)
7-38426976-C-A		not specified	Uncertain significance (Oct 20, 2023)
7-38432180-G-A			Likely benign (May 30, 2018)
7-38432190-G-A			Likely benign (Apr 06, 2018)
7-38436278-C-G			Benign (Dec 31, 2019)
7-38436322-C-T		not specified	Uncertain significance (Sep 16, 2021)
7-38461273-A-G			Likely benign (Dec 31, 2019)
7-38461286-G-T			Likely benign (Aug 14, 2018)
7-38461387-G-T		not specified	Uncertain significance (Jun 29, 2022)
7-38463004-C-T		not specified	Uncertain significance (Dec 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
AMPH	protein_coding	protein_coding	ENST00000356264	21	247863

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000170	1.00	125718	0	30	125748	0.000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.49	306	389	0.787	0.0000212	4492
Missense in Polyphen		129	180.41	0.71503		2184
Synonymous	-0.173	152	149	1.02	0.00000904	1354
Loss of Function	3.79	16	42.7	0.374	0.00000208	503

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000384	0.000384
Ashkenazi Jewish	0.000298	0.000298
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000107	0.000105
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May participate in mechanisms of regulated exocytosis in synapses and certain endocrine cell types. May control the properties of the membrane associated cytoskeleton.
• Pathway: Fc gamma R-mediated phagocytosis - Homo sapiens (human);Endocytosis - Homo sapiens (human);Monoamine Transport;Vesicle-mediated transport;Membrane Trafficking;Clathrin-mediated endocytosis;Internalization of ErbB1 (Consensus)

Recessive Scores

• pRec: 0.191

Intolerance Scores

• loftool: 0.696
• rvis_EVS: 0.23
• rvis_percentile_EVS: 68.52

Haploinsufficiency Scores

• pHI: 0.232
• hipred: Y
• hipred_score: 0.706
• ghis: 0.515

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.950

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Amph
• Phenotype: endocrine/exocrine gland phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Gene ontology

• Biological process: endocytosis;chemical synaptic transmission;synaptic vesicle endocytosis;membrane organization
• Cellular component: cytosol;plasma membrane;synaptic vesicle;actin cytoskeleton;cell junction;synaptic vesicle membrane;leading edge membrane
• Molecular function: protein binding;phospholipid binding