FHIP2A

protein-coding

FHF complex subunit HOOK interacting protein 2A, the group of FHF complex|Armadillo like helical domain containing

Gene summary

Predicted to be involved in protein transport along microtubule. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

KIAA1600
FAM160B1

MANE transcript

NM_020940.4

Inheritance

—

ClinVar variants

P:1U:71B:9

Top phenotype

FHIP2A-related condition

gnomAD constraint

pLI —, LoF o/e 0.12

Max pathogenic AF

—

Genomic locus

chr10:114,821,744-114,899,832

External References & Databases

Ensembl (ENSG00000151553)

Transcript & Mutation Effects

hg38 • Region Span ~78.1 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 FHIP2A variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 66

not providedTotal: 6

FHIP2A-related conditionTotal: 1

Syndromic intellectual disabilityTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_020940.4. 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			1 clinvar	2 clinvar		3
missense			64 clinvar	7 clinvar		71
nonsense		1 clinvar	1 clinvar			2
start loss						0
frameshift			2 clinvar			2
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	1	71	9	0	81

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 11 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_020940.4	RefSeq	NP_065991.3	17	MANE Select
ENST00000369248.9	Ensembl	ENSP00000358251.4	17	MANE Select
NM_001135051.2	RefSeq	NP_001128523.1	17	Standard
ENST00000369246.1	Ensembl	ENSP00000358249.1	3	Standard

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000369248
Coding exons: 17
Length: 78089
Individuals with no LoFs: 125726
Homozygous LoFs: 0
Heterozygous LoFs: 12
Defined: 125738
p: 0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.37	325	402	0.808	0.0000204	4987
Missense (PolyPhen)		68	128.01	0.5312		1611
Synonymous	-0.585	159	150	1.06	0.00000813	1469
Loss of Function	5.29	5	42.0	0.119	0.00000230	518

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.0000088	0.0000088	rare
South Asian	0.000099	0.000098	rare
Other	0.00034	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.0481
RVIS EVS: -0.75
RVIS percentile EVS: 13.58

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.455

Gene Damage Prediction

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