FAAP100

protein-coding

FA core complex associated protein 100

Gene summary

FAAP100 is a component of the Fanconi anemia (FA; MIM 277650) core complex and is required for core complex stability and FANCD2 (see MIM 227646) monoubiquitination (Ling et al., 2007 [PubMed 17396147]).[supplied by OMIM, Mar 2008]

Previous symbols:

C17orf70

MANE transcript

NM_025161.6

Inheritance

—

ClinVar variants

P:4U:151B:58

Top phenotype

Fanconi anemia, complementation group 10

gnomAD constraint

pLI —, LoF o/e 0.46

Max pathogenic AF

—

Genomic locus

chr17:81,539,885-81,553,961

External References & Databases

Ensembl (ENSG00000185504)

Transcript & Mutation Effects

hg38 • Region Span ~14.1 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to FAAP100 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 212

not providedTotal: 5

Fanconi anemia, complementation group 10Total: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_025161.6. Only rare variants are included.

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				37 clinvar		37
missense	1 clinvar		147 clinvar	21 clinvar		169
nonsense	1 clinvar		1 clinvar			2
start loss						0
frameshift	1 clinvar					1
splice donor/acceptor (+/-2bp)		1 clinvar	3 clinvar			4
Total	3	1	151	58	0	213

Highest pathogenic variant AF is 0.0000014113231

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 29 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_025161.6	RefSeq	NP_079437.5	9	MANE Select
ENST00000327787.13	Ensembl	ENSP00000333283.8	9	MANE Select
ENST00000425898.2	Ensembl	ENSP00000399674.2	5	Standard
ENST00000425898.3	Ensembl	ENSP00000399674.2	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Fanconi anemia pathway - Homo sapiens (human)
Fanconi Anemia Pathway
DNA Repair
Fanconi anemia pathway

Biological Process

interstrand cross-link repair

Molecular Function

DNA binding
protein binding

Cellular Component

nucleoplasm
cytosol
Fanconi anaemia nuclear complex
intermediate filament cytoskeleton

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000327787
Coding exons: 9
Length: 14077
Individuals with no LoFs: 125663
Homozygous LoFs: 0
Heterozygous LoFs: 31
Defined: 125694
p: 0.000123

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.693	472	516	0.914	0.0000326	5528
Missense (PolyPhen)		120	154.48	0.7768		1843
Synonymous	-2.51	294	244	1.20	0.0000169	1979
Loss of Function	2.59	12	26.3	0.456	0.00000146	293

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00031	0.00025	rare
Latino/Admixed American	0.00015	0.00014	rare
Ashkenazi Jewish	0.00021	0.00020	rare
East Asian	0.000054	0.000054	rare
Finnish	0.000093	0.000092	rare
European (Non-Finnish)	0.000081	0.000079	rare
South Asian	0.00023	0.00023	rare
Other	0.00019	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Plays a role in Fanconi anemia-associated DNA damage response network. Regulates FANCD2 monoubiquitination and the stability of the FA core complex. Induces chromosomal instability as well as hypersensitivity to DNA cross-linking agents, when repressed. {ECO:0000269|PubMed:17396147}.;

Recessive Scores

pRec: 0.160

Intolerance Scores

RVIS EVS: 0.36
RVIS percentile EVS: 74.71

Essentials

Essential (gene trap): N