FAM53A

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			3 clinvar	2 clinvar	4 clinvar	9
missense			90 clinvar	10 clinvar	6 clinvar	106
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	93	12	10	115

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 34 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001174070.3	RefSeq	NP_001167541.1	4	MANE Select
ENST00000308132.11	Ensembl	ENSP00000310057.6	4	MANE Select
NM_001013622.3	RefSeq	NP_001013644.1	4	Standard
NM_001297435.1	RefSeq	NP_001284364.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000308132
Coding exons: 4
Length: 66388
Individuals with no LoFs: 125708
Homozygous LoFs: 0
Heterozygous LoFs: 25
Defined: 125733
p: 0.0000994

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.445	244	225	1.08	0.0000156	2468
Missense (PolyPhen)		63	65.139	0.96717		776
Synonymous	-0.582	107	99.6	1.07	0.00000741	842
Loss of Function	1.22	5	8.96	0.558	4.49e-7	104

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00015	0.00012	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000079	0.000053	rare
South Asian	0.00053	0.00052	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May play an important role in neural development; the dorsomedial roof of the third ventricle. {ECO:0000250|UniProtKB:Q5ZKN5}.;

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0645

Gene Damage Prediction

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