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:154444140-154450654

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.

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.

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	3	1	5
missense		4	22	1		27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region			1			1
non coding				2		2
Total	0	4	24	6	1

Variants in FAM50A

This is a list of pathogenic ClinVar variants found in the FAM50A region.

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

Position	Type	Phenotype	Significance	ClinVar
X-154444302-A-C			Uncertain significance (Oct 05, 2023)
X-154444311-G-A			Uncertain significance (Oct 01, 2022)
X-154445673-C-T		Inborn genetic diseases	Likely benign (Jan 19, 2024)
X-154445714-G-C			Uncertain significance (May 07, 2019)
X-154445817-G-A		Inborn genetic diseases	Uncertain significance (Jun 24, 2022)
X-154446422-G-A		Inborn genetic diseases	Uncertain significance (May 23, 2024)
X-154446438-A-G		Inborn genetic diseases	Uncertain significance (Feb 28, 2024)
X-154446440-G-C			Uncertain significance (Jun 14, 2022)
X-154446444-G-T			Uncertain significance (Sep 01, 2022)
X-154446491-G-A		Inborn genetic diseases	Uncertain significance (Feb 27, 2024)
X-154446509-G-A		Inborn genetic diseases	Uncertain significance (Oct 06, 2021)
X-154446511-C-T		Armfield syndrome • FAM50A-related disorder	Uncertain significance (Aug 03, 2023)
X-154446519-A-G			Uncertain significance (Jun 23, 2021)
X-154446549-T-C		Inborn genetic diseases	Likely benign (Apr 06, 2024)
X-154448549-C-G			Uncertain significance (Jun 01, 2024)
X-154448552-G-A			Uncertain significance (Feb 15, 2022)
X-154448740-G-T			Uncertain significance (Dec 23, 2022)
X-154448903-C-T			Likely benign (Apr 01, 2023)
X-154448904-G-A		Inborn genetic diseases	Uncertain significance (Mar 31, 2024)
X-154448922-T-G		Armfield syndrome	Uncertain significance (May 07, 2020)
X-154448935-G-T			Uncertain significance (Sep 16, 2019)
X-154448940-C-T		Armfield syndrome	Conflicting classifications of pathogenicity (Mar 07, 2023)
X-154449685-G-T			Uncertain significance (Jun 10, 2021)
X-154449709-A-G		Inborn genetic diseases	Uncertain significance (Jul 09, 2021)
X-154449715-G-A		Inborn genetic diseases	Likely pathogenic (Aug 24, 2021)

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