GPATCH11

protein-coding

G-patch domain containing 11, the group of G-patch domain containing

Gene summary

Predicted to enable nucleic acid binding activity. Located in kinetochore and nucleoplasm. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

CCDC75

MANE transcript

NM_174931.4

Inheritance

ClinVar variants

P:4U:40

Top phenotype

neurodevelopmental disorder

gnomAD constraint

pLI —, LoF o/e 0.74

Max pathogenic AF

—

Genomic locus

chr2:37,084,518-37,099,244

External References & Databases

Ensembl (ENSG00000152133)

Transcript & Mutation Effects

hg38 • Region Span ~14.7 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

neurodevelopmental disorderSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0700092

Submitter: PanelApp Australia

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to GPATCH11 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 38

Early onset and severe retinal dystrophy with neurological impairment and facial dysmorphiaTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_174931.4. 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						0
missense			39 clinvar			39
nonsense	2 clinvar		1 clinvar			3
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)	2 clinvar					2
Total	4	0	40	0	0	44

Highest pathogenic variant AF is 0.00001275908

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 19 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_174931.4	RefSeq	NP_777591.4	8	MANE Select
ENST00000674370.2	Ensembl	ENSP00000501347.1	8	MANE Select
NM_001278505.2	RefSeq	NP_001265434.1	6	Standard
NM_001322249.4	RefSeq	NP_001309178.3	7	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

nucleic acid binding
protein binding

Cellular Component

kinetochore
condensed chromosome kinetochore

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000608836
Coding exons: 8
Length: 14794
Individuals with no LoFs: 125551
Homozygous LoFs: 0
Heterozygous LoFs: 10
Defined: 125561
p: 0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.0120	120	120	0.997	0.00000589	1700
Missense (PolyPhen)		30	36.799	0.81523		503
Synonymous	0.167	37	38.3	0.966	0.00000166	416
Loss of Function	1.01	13	17.6	0.739	0.00000106	219

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000056	0.000053	rare
South Asian	0.000034	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0943

Intolerance Scores

RVIS EVS: -0.07
RVIS percentile EVS: 48.12

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N

Gene Damage Prediction

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