FAM117B

family with sequence similarity 117 member B

Basic information

Region (hg38): 2:202634969-202769757

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.

• not_specified (70 variants)
• not_provided (1 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. These statistics are base on transcript: NM_000173511.4. 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			3			3
missense			72	1		73
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1			1
Total	0	0	76	1	0

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