FAM169A

family with sequence similarity 169 member A

Basic information

Region (hg38): 5:74777574-74866966

Links

ENSG00000198780NCBI:26049OMIM:615769HGNC:29138Uniprot:Q9Y6X4AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

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
clinvar
1
missense
26
clinvar
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)2320470
5-74781534-C-T not specified Uncertain significance (Mar 15, 2024)3277230
5-74781659-G-A not specified Uncertain significance (Aug 02, 2021)2209304
5-74781678-C-A not specified Uncertain significance (Nov 20, 2023)3091980
5-74781699-T-C not specified Uncertain significance (Dec 19, 2022)2336872
5-74781737-G-T not specified Uncertain significance (Oct 13, 2023)3091979
5-74781912-T-G not specified Uncertain significance (Feb 07, 2023)2462745
5-74781952-C-G not specified Uncertain significance (May 24, 2023)2551785
5-74782002-G-A not specified Uncertain significance (Aug 05, 2024)2343128
5-74783073-A-G not specified Uncertain significance (Jun 25, 2024)3511800
5-74796041-C-T not specified Uncertain significance (Nov 12, 2021)2364192
5-74796071-G-T not specified Uncertain significance (Oct 17, 2023)3091978
5-74796084-A-T not specified Uncertain significance (Nov 13, 2024)2323871
5-74796169-C-T not specified Uncertain significance (Jun 13, 2024)3277236
5-74800906-C-A not specified Uncertain significance (Jun 23, 2021)2233051
5-74800938-T-C not specified Uncertain significance (Jul 21, 2021)2276431
5-74800953-C-G not specified Uncertain significance (Jun 22, 2023)2605712
5-74800980-G-A not specified Uncertain significance (Apr 09, 2024)3277233
5-74801009-G-T not specified Uncertain significance (Jul 06, 2021)2365626
5-74801027-T-C not specified Uncertain significance (Jul 14, 2023)2599267
5-74801628-A-G not specified Uncertain significance (Dec 21, 2022)2363739
5-74804508-A-C not specified Uncertain significance (Dec 09, 2023)3091984
5-74804562-A-G Likely benign (Aug 01, 2022)2655532
5-74804570-C-T not specified Uncertain significance (Apr 29, 2024)3277231
5-74804578-G-A not specified Uncertain significance (Feb 28, 2024)3091983

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
FAM169Aprotein_codingprotein_codingENST00000389156 1289378
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.9990.000927124675031246780.0000120
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.422693430.7850.00001684388
Missense in Polyphen4997.5190.502461353
Synonymous-0.04741221211.010.000006061264
Loss of Function4.88333.50.08970.00000173419

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00003170.0000317
Ashkenazi Jewish0.000.00
East Asian0.00005580.0000556
Finnish0.000.00
European (Non-Finnish)0.000.00
Middle Eastern0.00005580.0000556
South Asian0.00003360.0000328
Other0.000.00

dbNSFP

Source: dbNSFP

Intolerance Scores

loftool
0.213
rvis_EVS
-0.2
rvis_percentile_EVS
38.98

Haploinsufficiency Scores

pHI
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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Fam169a
Phenotype

Gene ontology

Biological process
Cellular component
nuclear inner membrane
Molecular function