AFTPH

aftiphilin, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 2:64524299-64593005

Links

ENSG00000119844 ∙ NCBI:54812 ∙ OMIM:619628 ∙ HGNC:25951 ∙ Uniprot:Q6ULP2 ∙ 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 AFTPH gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the AFTPH 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						0
missense			49	4		53
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	49	4	0

Variants in AFTPH

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

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

Position	Type	Phenotype	Significance	ClinVar
2-64551527-A-G		not specified	Uncertain significance (Apr 20, 2024)
2-64551533-C-G		not specified	Uncertain significance (Jul 26, 2023)
2-64551540-T-A		not specified	Uncertain significance (Mar 19, 2024)
2-64551551-A-C		not specified	Uncertain significance (Jul 12, 2022)
2-64551634-C-A		not specified	Uncertain significance (Jul 15, 2021)
2-64551647-A-G		not specified	Uncertain significance (Mar 22, 2023)
2-64551680-A-G		not specified	Uncertain significance (Jan 03, 2024)
2-64551746-A-G		not specified	Uncertain significance (Apr 19, 2024)
2-64551962-A-T		not specified	Uncertain significance (May 27, 2022)
2-64551985-T-C		not specified	Uncertain significance (Sep 06, 2022)
2-64551994-G-A		not specified	Uncertain significance (Jun 16, 2024)
2-64552016-T-G		not specified	Uncertain significance (Mar 20, 2023)
2-64552018-C-G		not specified	Uncertain significance (Dec 06, 2021)
2-64552099-C-T		not specified	Likely benign (Jan 17, 2024)
2-64552133-A-G		not specified	Uncertain significance (Dec 16, 2021)
2-64552151-G-A		not specified	Uncertain significance (Aug 12, 2021)
2-64552180-A-G		not specified	Uncertain significance (Mar 25, 2024)
2-64552250-T-C		not specified	Uncertain significance (Nov 02, 2023)
2-64552259-G-A		not specified	Likely benign (Nov 16, 2021)
2-64552303-A-G		not specified	Uncertain significance (Jan 04, 2022)
2-64552308-A-C		not specified	Uncertain significance (Jul 05, 2022)
2-64552471-A-G		not specified	Uncertain significance (Mar 18, 2024)
2-64552537-G-A		not specified	Uncertain significance (Dec 12, 2023)
2-64552595-A-G		not specified	Uncertain significance (Jan 19, 2022)
2-64552598-C-A		not specified	Uncertain significance (Oct 25, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
AFTPH	protein_coding	protein_coding	ENST00000238855	9	68675

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000313	125503	0	1	125504	0.00000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.692	434	477	0.911	0.0000225	6215
Missense in Polyphen		72	122.12	0.5896		1657
Synonymous	0.333	167	173	0.968	0.00000860	1778
Loss of Function	5.22	1	33.7	0.0297	0.00000173	444

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000880	0.00000880
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in membrane trafficking.

Recessive Scores

• pRec: 0.0848

Intolerance Scores

• loftool: 0.265
• rvis_EVS: 0.18
• rvis_percentile_EVS: 66.24

Haploinsufficiency Scores

• pHI: 0.534
• hipred: N
• hipred_score: 0.487
• ghis: 0.526

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.313

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Aftph

Zebrafish Information Network

• Gene name: aftphb
• Affected structure: ventricular system
• Phenotype tag: abnormal
• Phenotype quality: hydrocephalic

Gene ontology

• Biological process: protein transport;intracellular transport
• Cellular component: nucleus;cytoplasm;Golgi apparatus;cytosol;AP-1 adaptor complex;trans-Golgi network membrane;intracellular membrane-bounded organelle
• Molecular function: protein transporter activity;clathrin binding