FAM104A

family with sequence similarity 104 member A

Basic information

Region (hg38): 17:73207352-73236753

Links

ENSG00000133193 ∙ NCBI:84923 ∙ ∙ HGNC:25918 ∙ Uniprot:Q969W3 ∙ 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 FAM104A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FAM104A 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						0
missense			18			18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			20	10	1	31
Total	0	0	38	10	1

Variants in FAM104A

This is a list of pathogenic ClinVar variants found in the FAM104A region.

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

Position	Type	Phenotype	Significance	ClinVar
17-73207704-C-T			Likely benign (Mar 01, 2022)
17-73208144-C-T			Benign (Jul 27, 2018)
17-73208293-TTTCTC-T		COG1 congenital disorder of glycosylation	Uncertain significance (Apr 11, 2022)
17-73208301-C-T		COG1 congenital disorder of glycosylation	Benign/Likely benign (Jan 25, 2024)
17-73208310-G-T			Likely benign (Feb 13, 2018)
17-73208316-T-C		COG1 congenital disorder of glycosylation	Uncertain significance (Jan 13, 2018)
17-73208318-T-TC		COG1 congenital disorder of glycosylation	Uncertain significance (Dec 17, 2023)
17-73208325-G-A		COG1 congenital disorder of glycosylation	Likely benign (Jun 15, 2023)
17-73208326-G-A		COG1 congenital disorder of glycosylation	Uncertain significance (Oct 28, 2021)
17-73208329-C-T		Inborn genetic diseases	Uncertain significance (May 30, 2024)
17-73208330-G-A		COG1 congenital disorder of glycosylation	Uncertain significance (Aug 31, 2022)
17-73208333-C-T		COG1 congenital disorder of glycosylation	Uncertain significance (Nov 05, 2022)
17-73208334-C-T		COG1 congenital disorder of glycosylation	Likely benign (Nov 28, 2021)
17-73208344-G-A		COG1 congenital disorder of glycosylation	Uncertain significance (Aug 12, 2022)
17-73208344-G-C		Inborn genetic diseases	Uncertain significance (Oct 26, 2021)
17-73208348-C-T		COG1 congenital disorder of glycosylation	Uncertain significance (Jun 13, 2021)
17-73208349-G-A		COG1 congenital disorder of glycosylation	Likely benign (Aug 10, 2023)
17-73208352-A-G		COG1 congenital disorder of glycosylation	Likely benign (Dec 11, 2023)
17-73208356-C-T		COG1 congenital disorder of glycosylation	Uncertain significance (Jul 12, 2022)
17-73208370-C-T		COG1 congenital disorder of glycosylation	Likely benign (Feb 18, 2023)
17-73208372-G-A		Inborn genetic diseases	Uncertain significance (Dec 20, 2023)
17-73208374-C-T		COG1 congenital disorder of glycosylation	Uncertain significance (May 04, 2021)
17-73208375-A-C		COG1 congenital disorder of glycosylation	Uncertain significance (Aug 07, 2021)
17-73208380-G-A		COG1 congenital disorder of glycosylation	Uncertain significance (Aug 05, 2022)
17-73208391-A-C		COG1 congenital disorder of glycosylation	Uncertain significance (Aug 30, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FAM104A	protein_coding	protein_coding	ENST00000405159	4	29401

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.246	0.727	124184	0	11	124195	0.0000443

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0216	124	123	1.01	0.00000649	1313
Missense in Polyphen		32	39.23	0.81571		419
Synonymous	-0.593	56	50.6	1.11	0.00000305	416
Loss of Function	1.85	2	7.47	0.268	3.31e-7	82

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000159	0.000154
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000569	0.0000538
Middle Eastern	0.00	0.00
South Asian	0.0000329	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 0.06
• rvis_percentile_EVS: 58.53

Haploinsufficiency Scores

• pHI: 0.162
• hipred: N
• hipred_score: 0.154
• ghis: 0.515

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.433

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fam104a
• Phenotype: homeostasis/metabolism phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Molecular function: protein binding