FAM3D

FAM3 metabolism regulating signaling molecule D

Basic information

Region (hg38): 3:58633946-58666834

Links

ENSG00000198643 ∙ NCBI:131177 ∙ OMIM:608619 ∙ HGNC:18665 ∙ Uniprot:Q96BQ1 ∙ 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 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		1
missense			15	1		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)
3-58634366-G-C		not specified	Uncertain significance (Oct 25, 2022)
3-58636306-G-T		not specified	Uncertain significance (Oct 08, 2024)
3-58636313-C-T		not specified	Uncertain significance (Dec 25, 2024)
3-58636314-C-T		not specified	Likely benign (Apr 24, 2024)
3-58636320-G-A		not specified	Uncertain significance (Mar 07, 2024)
3-58636371-C-T		not specified	Uncertain significance (Dec 13, 2023)
3-58636376-G-A		not specified	Uncertain significance (Jul 18, 2024)
3-58640159-A-G		not specified	Uncertain significance (Sep 09, 2021)
3-58640172-T-A		not specified	Uncertain significance (Mar 16, 2022)
3-58643691-C-T		not specified	Uncertain significance (Dec 25, 2024)
3-58643714-C-G		not specified	Uncertain significance (Feb 19, 2025)
3-58645540-C-T		not specified	Uncertain significance (Aug 10, 2021)
3-58645572-G-A		not specified	Uncertain significance (May 23, 2024)
3-58645607-A-G			Likely benign (Jul 23, 2018)
3-58653682-C-T		not specified	Uncertain significance (Aug 15, 2023)
3-58653692-G-A		not specified	Uncertain significance (Oct 26, 2022)
3-58653724-C-T		not specified	Uncertain significance (Jul 19, 2023)
3-58653742-G-A		not specified	Uncertain significance (Oct 09, 2024)
3-58653758-T-C		not specified	Uncertain significance (Feb 16, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FAM3D	protein_coding	protein_coding	ENST00000358781	9	32903

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000241	0.930	125735	0	13	125748	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.205	131	138	0.951	0.00000793	1476
Missense in Polyphen		51	57.855	0.88151		624
Synonymous	-1.25	62	50.7	1.22	0.00000325	406
Loss of Function	1.63	8	14.7	0.542	8.73e-7	149

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000582	0.0000582
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000264	0.0000264
Middle Eastern	0.000109	0.000109
South Asian	0.000164	0.000163
Other	0.000163	0.000163

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

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

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