FAM169A

family with sequence similarity 169 member A

Basic information

Region (hg38): 5:74777574-74866966

Links

ENSG00000198780 ∙ NCBI:26049 ∙ OMIM:615769 ∙ HGNC:29138 ∙ Uniprot:Q9Y6X4 ∙ 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 FAM169A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FAM169A 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				1		1
missense			26			26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	1	0

Variants in FAM169A

This is a list of pathogenic ClinVar variants found in the FAM169A region.

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

Position	Type	Phenotype	Significance	ClinVar
5-74781524-C-T		not specified	Uncertain significance (Oct 26, 2022)
5-74781534-C-T		not specified	Uncertain significance (Mar 15, 2024)
5-74781659-G-A		not specified	Uncertain significance (Aug 02, 2021)
5-74781678-C-A		not specified	Uncertain significance (Nov 20, 2023)
5-74781699-T-C		not specified	Uncertain significance (Dec 19, 2022)
5-74781737-G-T		not specified	Uncertain significance (Oct 13, 2023)
5-74781912-T-G		not specified	Uncertain significance (Feb 07, 2023)
5-74781952-C-G		not specified	Uncertain significance (May 24, 2023)
5-74782002-G-A		not specified	Uncertain significance (Aug 05, 2024)
5-74783073-A-G		not specified	Uncertain significance (Jun 25, 2024)
5-74796041-C-T		not specified	Uncertain significance (Nov 12, 2021)
5-74796071-G-T		not specified	Uncertain significance (Oct 17, 2023)
5-74796084-A-T		not specified	Uncertain significance (Nov 13, 2024)
5-74796169-C-T		not specified	Uncertain significance (Jun 13, 2024)
5-74800906-C-A		not specified	Uncertain significance (Jun 23, 2021)
5-74800938-T-C		not specified	Uncertain significance (Jul 21, 2021)
5-74800953-C-G		not specified	Uncertain significance (Jun 22, 2023)
5-74800980-G-A		not specified	Uncertain significance (Apr 09, 2024)
5-74801009-G-T		not specified	Uncertain significance (Jul 06, 2021)
5-74801027-T-C		not specified	Uncertain significance (Jul 14, 2023)
5-74801628-A-G		not specified	Uncertain significance (Dec 21, 2022)
5-74804508-A-C		not specified	Uncertain significance (Dec 09, 2023)
5-74804562-A-G			Likely benign (Aug 01, 2022)
5-74804570-C-T		not specified	Uncertain significance (Apr 29, 2024)
5-74804578-G-A		not specified	Uncertain significance (Feb 28, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FAM169A	protein_coding	protein_coding	ENST00000389156	12	89378

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.000927	124675	0	3	124678	0.0000120

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.42	269	343	0.785	0.0000168	4388
Missense in Polyphen		49	97.519	0.50246		1353
Synonymous	-0.0474	122	121	1.01	0.00000606	1264
Loss of Function	4.88	3	33.5	0.0897	0.00000173	419

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000317	0.0000317
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000558	0.0000556
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.0000558	0.0000556
South Asian	0.0000336	0.0000328
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.213
• rvis_EVS: -0.2
• rvis_percentile_EVS: 38.98

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.420
• ghis: 0.561

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.648

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fam169a

Gene ontology

• Cellular component: nuclear inner membrane