FAM117A

family with sequence similarity 117 member A

Basic information

Region (hg38): 17:49710332-49789180

Links

ENSG00000121104 ∙ NCBI:81558 ∙ ∙ HGNC:24179 ∙ Uniprot:Q9C073 ∙ 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 FAM117A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FAM117A 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			23	1		24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	1	0

Variants in FAM117A

This is a list of pathogenic ClinVar variants found in the FAM117A region.

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

Position	Type	Phenotype	Significance	ClinVar
17-49711262-A-G		not specified	Uncertain significance (Jan 24, 2023)
17-49711361-C-T		not specified	Uncertain significance (Sep 29, 2023)
17-49711535-G-T		not specified	Uncertain significance (Aug 05, 2024)
17-49716184-G-A		not specified	Uncertain significance (Oct 25, 2024)
17-49716240-C-T		not specified	Uncertain significance (Apr 01, 2024)
17-49716283-C-T		not specified	Uncertain significance (Apr 24, 2024)
17-49717546-C-T		not specified	Uncertain significance (May 05, 2023)
17-49717555-G-A		not specified	Uncertain significance (Feb 05, 2024)
17-49717564-C-T		not specified	Uncertain significance (Dec 20, 2023)
17-49717641-A-C		not specified	Uncertain significance (Feb 28, 2023)
17-49717642-G-A		not specified	Uncertain significance (Jan 23, 2024)
17-49717654-G-T		not specified	Uncertain significance (Jun 04, 2024)
17-49717690-G-A		not specified	Uncertain significance (Jul 19, 2023)
17-49719854-C-T		not specified	Uncertain significance (Sep 26, 2023)
17-49719884-G-C		not specified	Uncertain significance (Jun 29, 2023)
17-49720349-G-A		not specified	Uncertain significance (Dec 21, 2023)
17-49720350-G-T		not specified	Uncertain significance (Dec 03, 2021)
17-49720361-G-T		not specified	Uncertain significance (Apr 15, 2024)
17-49720391-T-C		not specified	Likely benign (Oct 13, 2023)
17-49720393-C-T		not specified	Uncertain significance (Apr 13, 2023)
17-49720394-G-A		not specified	Uncertain significance (Jul 13, 2021)
17-49722537-G-A		not specified	Uncertain significance (Jul 12, 2022)
17-49732574-A-G		not specified	Uncertain significance (Jun 17, 2022)
17-49732627-C-T		not specified	Uncertain significance (Jan 23, 2024)
17-49732657-C-T		not specified	Uncertain significance (Apr 08, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FAM117A	protein_coding	protein_coding	ENST00000240364	8	78849

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000597	0.976	125734	0	13	125747	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.49	171	235	0.727	0.0000140	2866
Missense in Polyphen		51	98.721	0.51661		1093
Synonymous	0.726	84	92.9	0.904	0.00000509	994
Loss of Function	2.03	10	19.7	0.508	0.00000135	200

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000156	0.000152
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000545	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000718	0.0000703
Middle Eastern	0.0000545	0.0000544
South Asian	0.0000339	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.288
• rvis_EVS: -0.18
• rvis_percentile_EVS: 40.16

Haploinsufficiency Scores

• pHI: 0.394
• hipred: N
• hipred_score: 0.375
• ghis: 0.519

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.757

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fam117a