AFM

afamin

Basic information

Region (hg38): 4:73481744-73504001

Links

ENSG00000079557 ∙ NCBI:173 ∙ OMIM:104145 ∙ HGNC:316 ∙ Uniprot:P43652 ∙ 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 AFM gene.

• Inborn genetic diseases (36 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the AFM 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			35	1		36
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	35	1	0

Variants in AFM

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

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

Position	Type	Phenotype	Significance	ClinVar
4-73481854-C-T		not specified	Uncertain significance (Jul 11, 2023)
4-73483951-T-G		not specified	Uncertain significance (Oct 02, 2023)
4-73483958-C-A		not specified	Uncertain significance (Aug 21, 2023)
4-73484292-G-C		not specified	Uncertain significance (Jul 26, 2023)
4-73484325-G-T		not specified	Uncertain significance (May 04, 2022)
4-73484358-G-A		not specified	Uncertain significance (May 09, 2022)
4-73484365-C-T		not specified	Uncertain significance (Apr 25, 2022)
4-73484377-G-T		not specified	Uncertain significance (Aug 10, 2023)
4-73485941-T-A		not specified	Uncertain significance (Dec 16, 2022)
4-73486000-C-T		not specified	Uncertain significance (Aug 14, 2023)
4-73486039-G-C		not specified	Uncertain significance (Mar 29, 2022)
4-73486994-C-A		not specified	Uncertain significance (Jan 16, 2024)
4-73487025-G-A		not specified	Uncertain significance (Jan 16, 2024)
4-73487083-A-C		not specified	Uncertain significance (Sep 27, 2022)
4-73487740-A-G		not specified	Uncertain significance (May 02, 2023)
4-73488638-C-T		not specified	Uncertain significance (Sep 16, 2021)
4-73488689-T-C		not specified	Uncertain significance (Feb 09, 2023)
4-73488715-G-T		not specified	Uncertain significance (Jan 22, 2024)
4-73488751-C-T		not specified	Uncertain significance (May 18, 2022)
4-73492020-G-A		not specified	Uncertain significance (Aug 10, 2021)
4-73492027-T-A		not specified	Uncertain significance (Nov 08, 2022)
4-73492035-G-A		not specified	Uncertain significance (Apr 19, 2023)
4-73492049-C-G		not specified	Likely benign (Dec 27, 2023)
4-73492083-C-A		not specified	Uncertain significance (Aug 17, 2021)
4-73495309-T-G		not specified	Uncertain significance (Apr 22, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
AFM	protein_coding	protein_coding	ENST00000226355	14	22292

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.27e-19	0.00534	125452	0	294	125746	0.00117

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.578	338	309	1.09	0.0000150	4007
Missense in Polyphen		110	95.835	1.1478		1340
Synonymous	-0.652	117	108	1.08	0.00000549	1041
Loss of Function	0.221	29	30.3	0.957	0.00000143	418

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00139	0.00139
Ashkenazi Jewish	0.00458	0.00457
East Asian	0.00544	0.00545
Finnish	0.00181	0.00180
European (Non-Finnish)	0.000507	0.000501
Middle Eastern	0.00544	0.00545
South Asian	0.000553	0.000523
Other	0.000820	0.000815

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Functions as carrier for hydrophobic molecules in body fluids (Probable). Essential for the solubility and activity of lipidated Wnt family members, including WNT1, WNT2B, WNT3, WNT3A, WNT5A, WNT7A, WNT7B, WNT8, WNT9A, WNT9B, WNT10A and WNT10B (PubMed:26902720). Binds vitamin E (PubMed:15952736, PubMed:12463752). May transport vitamin E in body fluids under conditions where the lipoprotein system is not sufficient (PubMed:15952736). May be involved in the transport of vitamin E across the blood-brain barrier (PubMed:19046407). {ECO:0000269|PubMed:12463752, ECO:0000269|PubMed:15952736, ECO:0000269|PubMed:19046407, ECO:0000269|PubMed:26902720, ECO:0000305}.

Recessive Scores

• pRec: 0.127

Intolerance Scores

• loftool: 0.863
• rvis_EVS: 0.49
• rvis_percentile_EVS: 79.46

Haploinsufficiency Scores

• pHI: 0.152
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0327

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Afm
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); hematopoietic system phenotype; limbs/digits/tail phenotype

Gene ontology

• Biological process: protein stabilization;vitamin transport;protein transport within extracellular region
• Cellular component: extracellular region;extracellular space;extracellular exosome;blood microparticle
• Molecular function: protein binding;vitamin E binding