ATP5MF-PTCD1

protein-coding

ATP5MF-PTCD1 readthrough

Gene summary

This locus represents naturally occurring read-through transcription between the ATP5J2 (ATP synthase, H+ transporting, mitochondrial Fo complex, subunit F2) and PTCD1 (pentatricopeptide repeat domain 1) genes on chromosome 7. The read-through transcript encodes a fusion protein that shares sequence identity with each individual gene product. [provided by RefSeq, Nov 2010]

Previous symbols:

ATP5J2-PTCD1

MANE transcript

N/A

Inheritance

—

ClinVar variants

U:3B:10

Top phenotype

Inborn genetic diseases

gnomAD constraint

pLI —, LoF o/e 0.82

Max pathogenic AF

—

Genomic locus

chr7:99,419,749-99,466,197

External References & Databases

Ensembl (ENSG00000248919)

NCBI Gene (100526740)

HGNC:38844

GenCC

ClinVar (ATP5MF-PTCD1)

Transcript & Mutation Effects

hg38 • Region Span ~46.4 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 ATP5MF-PTCD1 variants in ClinVar

4 Conditions Cataloged

not providedTotal: 11

Inborn genetic diseasesTotal: 4

Kabuki syndrome 1Total: 1

not specifiedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript . 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	4 clinvar	5
missense			2 clinvar	3 clinvar	2 clinvar	7
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	3	4	6	13

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 3 of 3 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001198879.2	RefSeq	NP_001185808.1	9	Standard
ENST00000413834.5	Ensembl	ENSP00000400168.1	9	Standard
ENST00000451138.1	Ensembl	ENSP00000416954.1	3	Standard

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000413834
Coding exons: 9
Length: 46449
Individuals with no LoFs: 125651
Homozygous LoFs: 0
Heterozygous LoFs: 97
Defined: 125748
p: 0.000386

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.560	466	433	1.08	0.0000283	4845
Missense (PolyPhen)		138	136.56	1.0106		1560
Synonymous	-2.09	234	197	1.19	0.0000139	1556
Loss of Function	0.924	24	29.4	0.816	0.00000162	332

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00025	0.00025	rare
Latino/Admixed American	0.00026	0.00026	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00060	0.00060	rare
Finnish	0.00023	0.00023	rare
European (Non-Finnish)	0.00033	0.00033	rare
South Asian	0.00098	0.00098	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

RVIS EVS: 0.3
RVIS percentile EVS: 71.7