XNDC1N

protein-coding

XRCC1 N-terminal domain containing 1, N-terminal like

Gene summary

Predicted to enable damaged DNA binding activity. Predicted to be involved in single strand break repair. Located in nucleolus. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001375847.2

Inheritance

—

ClinVar variants

U:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.12

Max pathogenic AF

—

Genomic locus

chr11:71,865,504-71,928,654

External References & Databases

Ensembl (ENSG00000254469)

NCBI Gene (100133315)

Transcript & Mutation Effects

hg38 • Region Span ~63.2 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 XNDC1N variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001375847.2. 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			1
missense						0
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	1	0	0	1

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 16 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001375847.2	RefSeq	NP_001362776.1	5	MANE Select
ENST00000679412.2	Ensembl	ENSP00000506430.1	5	MANE Select
NM_001375848.2	RefSeq	NP_001362777.1	5	Standard
ENST00000528184.1	Ensembl	ENSP00000435720.1	2	Standard

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000528511
Coding exons: 5
Length: 63146
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.21	79	116	0.683	0.00000622	1323
Missense (PolyPhen)		23	41.124	0.55928		472
Synonymous	1.54	33	46.3	0.712	0.00000235	433
Loss of Function	-0.361	11	9.78	1.12	5.65e-7	108

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent