FAM117B

family with sequence similarity 117 member B

Basic information

Region (hg38): 2:202634968-202769757

Previous symbols: [ "ALS2CR13" ]

Links

ENSG00000138439 ∙ NCBI:150864 ∙ ∙ HGNC:14440 ∙ Uniprot:Q6P1L5 ∙ 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 FAM117B gene.

• Inborn genetic diseases (28 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FAM117B 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			27	1		28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	27	1	0

Variants in FAM117B

This is a list of pathogenic ClinVar variants found in the FAM117B region.

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

Position	Type	Phenotype	Significance	ClinVar
2-202635206-C-T		not specified	Uncertain significance (May 08, 2023)
2-202635221-A-G		not specified	Uncertain significance (Feb 14, 2023)
2-202635242-G-A		not specified	Uncertain significance (Jun 16, 2023)
2-202635323-C-G		not specified	Uncertain significance (Oct 03, 2022)
2-202635365-G-A		not specified	Uncertain significance (May 18, 2022)
2-202635437-G-A		not specified	Uncertain significance (Sep 15, 2022)
2-202635444-G-A		not specified	Uncertain significance (Mar 20, 2023)
2-202635485-A-G		not specified	Uncertain significance (Dec 06, 2021)
2-202635525-C-A		not specified	Uncertain significance (Mar 08, 2024)
2-202635546-C-T		not specified	Uncertain significance (Feb 17, 2024)
2-202635560-C-T		not specified	Uncertain significance (Jun 29, 2023)
2-202635645-C-A		not specified	Uncertain significance (Jul 31, 2023)
2-202635726-C-T		not specified	Uncertain significance (Feb 23, 2023)
2-202635729-C-T		not specified	Uncertain significance (Jan 23, 2023)
2-202635739-C-G		not specified	Uncertain significance (Mar 22, 2022)
2-202635749-C-T		not specified	Uncertain significance (Nov 30, 2022)
2-202695914-C-G		not specified	Uncertain significance (Aug 30, 2021)
2-202695929-G-A		not specified	Uncertain significance (Feb 28, 2023)
2-202695956-C-T		not specified	Uncertain significance (Sep 14, 2021)
2-202724920-G-A		not specified	Uncertain significance (Oct 20, 2023)
2-202724971-C-T		not specified	Uncertain significance (Jul 14, 2021)
2-202724972-G-A		not specified	Uncertain significance (Nov 12, 2021)
2-202724995-G-A		not specified	Uncertain significance (Dec 20, 2021)
2-202755541-C-T		not specified	Uncertain significance (Jul 06, 2021)
2-202755574-C-G		not specified	Uncertain significance (Jan 23, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FAM117B	protein_coding	protein_coding	ENST00000392238	8	134580

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00901	0.989	125693	0	54	125747	0.000215

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.55	183	252	0.726	0.0000139	3762
Missense in Polyphen		50	111.18	0.44973		1300
Synonymous	0.186	88	90.3	0.975	0.00000476	1257
Loss of Function	2.67	7	19.9	0.353	0.00000119	237

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000578	0.0000578
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.0000553	0.0000544
Finnish	0.00125	0.00125
European (Non-Finnish)	0.000169	0.000167
Middle Eastern	0.0000553	0.0000544
South Asian	0.00	0.00
Other	0.000662	0.000652

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.110

Haploinsufficiency Scores

• pHI: 0.404
• hipred: Y
• hipred_score: 0.554
• ghis: 0.657

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.423

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fam117b
• Phenotype: homeostasis/metabolism phenotype; vision/eye phenotype; skeleton phenotype

Gene ontology

• Molecular function: protein binding