FAM114A2

family with sequence similarity 114 member A2

Basic information

Region (hg38): 5:153990148-154038936

Previous symbols: [ "C5orf3" ]

Links

ENSG00000055147 ∙ NCBI:10827 ∙ ∙ HGNC:1333 ∙ Uniprot:Q9NRY5 ∙ 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 FAM114A2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FAM114A2 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			38	6	1	45
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	38	6	1

Variants in FAM114A2

This is a list of pathogenic ClinVar variants found in the FAM114A2 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-153992986-A-G		not specified	Likely benign (Jan 09, 2023)
5-153993001-C-A		not specified	Likely benign (Nov 07, 2023)
5-153993005-G-C		not specified	Uncertain significance (Apr 17, 2024)
5-153993102-G-C		not specified	Uncertain significance (May 25, 2022)
5-153994956-T-C		not specified	Uncertain significance (Dec 19, 2023)
5-153997846-G-A		not specified	Uncertain significance (Jan 21, 2025)
5-153997852-T-G		not specified	Uncertain significance (Nov 08, 2024)
5-154002258-G-A		not specified	Uncertain significance (Oct 03, 2023)
5-154002263-T-C		not specified	Likely benign (May 21, 2024)
5-154002270-T-C		not specified	Uncertain significance (Aug 04, 2024)
5-154002369-G-A		not specified	Uncertain significance (Apr 25, 2023)
5-154002380-G-A		not specified	Uncertain significance (Aug 16, 2021)
5-154011245-G-A		not specified	Uncertain significance (Jan 10, 2022)
5-154011264-A-C		not specified	Uncertain significance (Dec 01, 2022)
5-154011276-G-C		not specified	Uncertain significance (May 30, 2023)
5-154011282-A-G		not specified	Uncertain significance (Jan 04, 2024)
5-154011294-T-C		not specified	Uncertain significance (May 11, 2022)
5-154011297-T-C		not specified	Uncertain significance (Jul 12, 2023)
5-154011314-T-G		not specified	Uncertain significance (Dec 13, 2024)
5-154026476-A-G		not specified	Uncertain significance (Aug 10, 2024)
5-154026480-T-A		not specified	Uncertain significance (Jan 17, 2023)
5-154027211-C-A		not specified	Uncertain significance (Jan 23, 2025)
5-154027238-C-T		not specified	Uncertain significance (Oct 09, 2024)
5-154027261-G-A		not specified	Uncertain significance (Dec 16, 2024)
5-154027280-C-T		not specified	Likely benign (Nov 08, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FAM114A2	protein_coding	protein_coding	ENST00000351797	13	48809

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.23e-10	0.679	125613	0	133	125746	0.000529

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.380	270	253	1.07	0.0000122	3269
Missense in Polyphen		82	80.025	1.0247		1068
Synonymous	-1.27	112	96.2	1.16	0.00000494	985
Loss of Function	1.40	18	25.7	0.701	0.00000126	335

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00196	0.00195
Ashkenazi Jewish	0.00	0.00
East Asian	0.000226	0.000217
Finnish	0.000606	0.000601
European (Non-Finnish)	0.000365	0.000360
Middle Eastern	0.000226	0.000217
South Asian	0.000989	0.000980
Other	0.000512	0.000489

dbNSFP

Source: dbNSFP

• Pathway: Disease;Signaling by BRAF and RAF fusions;Oncogenic MAPK signaling;Diseases of signal transduction (Consensus)

Recessive Scores

• pRec: 0.0837

Intolerance Scores

• loftool: 0.935
• rvis_EVS: -0.18
• rvis_percentile_EVS: 40.45

Haploinsufficiency Scores

• pHI: 0.104
• hipred: N
• hipred_score: 0.251
• ghis: 0.558

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.143

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fam114a2

Gene ontology

• Biological process: biological_process
• Cellular component: cellular_component
• Molecular function: purine nucleotide binding