FAM114A1

family with sequence similarity 114 member A1, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 4:38867677-38945739

Links

ENSG00000197712 ∙ NCBI:92689 ∙ ∙ HGNC:25087 ∙ Uniprot:Q8IWE2 ∙ 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 FAM114A1 gene.

• not_specified (68 variants)
• not_provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FAM114A1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000138389.4. 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				1		1
missense			66	3		69
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	66	4	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FAM114A1	protein_coding	protein_coding	ENST00000358869	13	78063

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.47e-20	0.000733	125546	0	201	125747	0.000800

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.490	282	306	0.921	0.0000161	3654
Missense in Polyphen		91	111.67	0.81487		1263
Synonymous	-0.256	124	120	1.03	0.00000733	1084
Loss of Function	-0.429	29	26.6	1.09	0.00000112	366

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00430	0.00428
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000545	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000355	0.000352
Middle Eastern	0.0000545	0.0000544
South Asian	0.000855	0.000850
Other	0.00116	0.00114

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in neuronal cell development. {ECO:0000250}.

Intolerance Scores

• loftool: 0.837
• rvis_EVS: 0.36
• rvis_percentile_EVS: 74.66

Haploinsufficiency Scores

• pHI: 0.120
• hipred: N
• hipred_score: 0.216
• ghis: 0.509

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.171

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fam114a1

Gene ontology

• Cellular component: nucleus;nucleoplasm;Golgi apparatus;cytosol
• Molecular function: protein binding