FRA10AC1

FRA10A associated CGG repeat 1, the group of Spliceosomal C complex

Basic information

Region (hg38): 10:93667883-93702592

Previous symbols: [ "C10orf4" ]

Links

ENSG00000148690 ∙ NCBI:118924 ∙ OMIM:608866 ∙ HGNC:1162 ∙ Uniprot:Q70Z53 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• neurodevelopmental disorder with growth retardation, dysmorphic facies, and corpus callosum abnormalities (Moderate), mode of inheritance: AR
• neurodevelopmental disorder with growth retardation, dysmorphic facies, and corpus callosum abnormalities (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Neurodevelopmental disorder with growth retardation, dysmorphic facies, and corpus callosum abnormalitie	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Craniofacial; Musculoskeletal; Neurologic	34694367; 35821753; 35871492

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the FRA10AC1 gene.

• Neurodevelopmental disorder with growth retardation, dysmorphic facies, and corpus callosum abnormalities (3 variants)
• not provided (2 variants)
• See cases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FRA10AC1 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			15	2		17
nonsense	2					2
start loss						0
frameshift	1					1
inframe indel	1					1
splice donor/acceptor (+/-2bp)		1	1			2
splice region						0
non coding						0
Total	4	1	16	2	0

Highest pathogenic variant AF is 0.0000463

Variants in FRA10AC1

This is a list of pathogenic ClinVar variants found in the FRA10AC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-93676664-T-C		Inborn genetic diseases	Uncertain significance (Jan 18, 2025)
10-93681495-T-G			Uncertain significance (Apr 07, 2023)
10-93681512-G-A		Inborn genetic diseases	Uncertain significance (May 20, 2024)
10-93681588-T-C		Inborn genetic diseases	Likely benign (Sep 09, 2021)
10-93684062-T-C		Inborn genetic diseases	Uncertain significance (May 24, 2024)
10-93685300-C-T		Inborn genetic diseases	Uncertain significance (Apr 08, 2024)
10-93685309-T-TTAAA		Neurodevelopmental disorder with growth retardation, dysmorphic facies, and corpus callosum abnormalities	Pathogenic (Nov 04, 2022)
10-93685311-T-C			Uncertain significance (Apr 07, 2023)
10-93687418-ACTT-A		Neurodevelopmental disorder with growth retardation, dysmorphic facies, and corpus callosum abnormalities	Pathogenic (May 27, 2025)
10-93687434-G-A		Neurodevelopmental disorder with growth retardation, dysmorphic facies, and corpus callosum abnormalities • See cases	Pathogenic (Aug 14, 2024)
10-93692034-T-G		Inborn genetic diseases	Uncertain significance (Dec 03, 2024)
10-93692066-A-T		FRA10AC1-related condition	Uncertain significance (Sep 11, 2024)
10-93692645-C-T		Neurodevelopmental disorder with growth retardation, dysmorphic facies, and corpus callosum abnormalities	Likely pathogenic (Mar 29, 2024)
10-93692698-G-A		Neurodevelopmental disorder with growth retardation, dysmorphic facies, and corpus callosum abnormalities	Likely pathogenic (Feb 01, 2024)
10-93692719-T-C		Inborn genetic diseases	Uncertain significance (Sep 22, 2023)
10-93694867-C-T		Inborn genetic diseases	Uncertain significance (Apr 25, 2022)
10-93694870-T-C		Inborn genetic diseases	Likely benign (Mar 15, 2024)
10-93694874-A-C		Inborn genetic diseases	Uncertain significance (Jun 04, 2024)
10-93694874-A-G		Inborn genetic diseases	Uncertain significance (Dec 08, 2023)
10-93694925-T-C		Inborn genetic diseases	Uncertain significance (Nov 07, 2024)
10-93698130-G-C		Neurodevelopmental disorder with growth retardation, dysmorphic facies, and corpus callosum abnormalities	Uncertain significance (Sep 14, 2024)
10-93698144-T-C		Inborn genetic diseases	Uncertain significance (Jan 23, 2023)
10-93698183-T-G		See cases	Uncertain significance (Nov 25, 2022)
10-93698331-TGG-T			Uncertain significance (Nov 16, 2024)
10-93698346-T-C		Inborn genetic diseases	Uncertain significance (Dec 11, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FRA10AC1	protein_coding	protein_coding	ENST00000359204	13	34690

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.91e-10	0.370	125684	0	56	125740	0.000223

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.475	128	144	0.889	0.00000659	2084
Missense in Polyphen		35	45.496	0.76929		656
Synonymous	2.68	24	47.4	0.506	0.00000222	464
Loss of Function	0.962	17	21.9	0.778	0.00000102	320

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000676	0.000639
Ashkenazi Jewish	0.00	0.00
East Asian	0.000639	0.000598
Finnish	0.0000467	0.0000462
European (Non-Finnish)	0.000203	0.000193
Middle Eastern	0.000639	0.000598
South Asian	0.000315	0.000294
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0830

Intolerance Scores

• rvis_EVS: 0.75
• rvis_percentile_EVS: 86.57

Haploinsufficiency Scores

• pHI: 0.122
• hipred: Y
• hipred_score: 0.675
• ghis: 0.464

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.731

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fra10ac1

Gene ontology

• Cellular component: nucleus
• Molecular function: protein binding