FAM3D

FAM3 metabolism regulating signaling molecule D

Basic information

Region (hg38): 3:58633946-58666834

Links

ENSG00000198643NCBI:131177OMIM:608619HGNC:18665Uniprot:Q96BQ1AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the FAM3D gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FAM3D 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
15
clinvar
1
clinvar
16
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 15 2 0

Variants in FAM3D

This is a list of pathogenic ClinVar variants found in the FAM3D region.

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

Position Type Phenotype Significance ClinVar
3-58634356-T-C not specified Uncertain significance (Feb 11, 2025)2375800
3-58634366-G-C not specified Uncertain significance (Oct 25, 2022)2405525
3-58636306-G-T not specified Uncertain significance (Oct 08, 2024)3512247
3-58636313-C-T not specified Uncertain significance (Dec 25, 2024)3847713
3-58636314-C-T not specified Likely benign (Apr 24, 2024)3277424
3-58636320-G-A not specified Uncertain significance (Mar 07, 2024)3092416
3-58636371-C-T not specified Uncertain significance (Dec 13, 2023)3092415
3-58636376-G-A not specified Uncertain significance (Jul 18, 2024)2354479
3-58640159-A-G not specified Uncertain significance (Sep 09, 2021)2248895
3-58640172-T-A not specified Uncertain significance (Mar 16, 2022)2278833
3-58643691-C-T not specified Uncertain significance (Dec 25, 2024)3847712
3-58643714-C-G not specified Uncertain significance (Feb 19, 2025)3847714
3-58645540-C-T not specified Uncertain significance (Aug 10, 2021)2227046
3-58645572-G-A not specified Uncertain significance (May 23, 2024)3277425
3-58645607-A-G Likely benign (Jul 23, 2018)786502
3-58653682-C-T not specified Uncertain significance (Aug 15, 2023)2599991
3-58653692-G-A not specified Uncertain significance (Oct 26, 2022)2375130
3-58653724-C-T not specified Uncertain significance (Jul 19, 2023)2590241
3-58653742-G-A not specified Uncertain significance (Oct 09, 2024)3512246
3-58653758-T-C not specified Uncertain significance (Feb 16, 2023)2469328

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
FAM3Dprotein_codingprotein_codingENST00000358781 932903
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.0002410.9301257350131257480.0000517
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.2051311380.9510.000007931476
Missense in Polyphen5157.8550.88151624
Synonymous-1.256250.71.220.00000325406
Loss of Function1.63814.70.5428.73e-7149

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00005820.0000582
Ashkenazi Jewish0.000.00
East Asian0.0001090.000109
Finnish0.000.00
European (Non-Finnish)0.00002640.0000264
Middle Eastern0.0001090.000109
South Asian0.0001640.000163
Other0.0001630.000163

dbNSFP

Source: dbNSFP

Recessive Scores

pRec
0.0952

Intolerance Scores

loftool
0.642
rvis_EVS
0.26
rvis_percentile_EVS
70.44

Haploinsufficiency Scores

pHI
0.0529
hipred
N
hipred_score
0.145
ghis
0.380

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.450

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Oit1
Phenotype
behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan);

Gene ontology

Biological process
regulation of signaling receptor activity;negative regulation of insulin secretion;negative regulation of glucagon secretion
Cellular component
extracellular region
Molecular function
cytokine activity