FAM50A

family with sequence similarity 50 member A, the group of MicroRNA protein coding host genes|Spliceosomal P complex|Spliceosomal C complex

Basic information

Region (hg38): X:154444141-154450654

Links

ENSG00000071859 ∙ NCBI:9130 ∙ OMIM:300453 ∙ HGNC:18786 ∙ Uniprot:Q14320 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Armfield syndrome (Moderate), mode of inheritance: XL

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Intellectual disability disorder, X-linked, syndrome, Armfield type	XL	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Craniofacial; Dental; Dermatologic; Musculoskeletal; Neurologic	10398235; 32703943

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the FAM50A gene.

• not_provided (41 variants)
• Inborn_genetic_diseases (13 variants)
• Armfield_syndrome (8 variants)
• FAM50A-related_disorder (3 variants)
• not_specified (3 variants)
• Intellectual_disability (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FAM50A gene is commonly pathogenic or not. These statistics are base on transcript: NM_000004699.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			2	6	1	9
missense		5	34	3		42
nonsense			1			1
start loss			1			1
frameshift						0
splice donor/acceptor (+/-2bp)			1			1
Total	0	5	39	9	1

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FAM50A	protein_coding	protein_coding	ENST00000393600	13	6530

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.979	0.0209	125736	1	1	125738	0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.02	44	147	0.299	0.0000128	2278
Missense in Polyphen		10	56.655	0.17651		781
Synonymous	0.266	54	56.5	0.955	0.00000511	569
Loss of Function	3.51	1	16.3	0.0615	0.00000123	278

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000365	0.0000365
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000122	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be a DNA-binding protein or transcriptional factor. {ECO:0000269|PubMed:9339379}.

Recessive Scores

• pRec: 0.141

Intolerance Scores

• loftool: 0.171
• rvis_EVS: -0.01
• rvis_percentile_EVS: 53.19

Haploinsufficiency Scores

• pHI: 0.0908
• hipred: Y
• hipred_score: 0.675
• ghis: 0.534

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.307

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fam50a

Gene ontology

• Biological process: spermatogenesis
• Cellular component: nucleus;nucleoplasm
• Molecular function: RNA binding