# NM_004628.5(XPC):c.1509C>T (p.Ser503=)

https://sugi.bio/variant/xpc-p-ser503

## Summary

**XPC p.Ser503= (c.1509C>T)** is classified **Conflicting classifications of pathogenicity** in XPC (ClinVar, Conflicting submitters, 6 submitters; last evaluated 2025-12-01). Very rare (popmax 0.00636%, nfe); Associated with xeroderma pigmentosum group C.

**At a glance:** Conflicting classifications of pathogenicity · review: Conflicting submitters · rsID rs760867012 · 6 submitters · 2 linked conditions · very rare (popmax 0.00636%, nfe)

## For patients & families {#patients}

This is a change in the XPC gene that is of uncertain or conflicting significance (submitters disagree on it), submitted by 6 submitters, and is linked to xeroderma pigmentosum group C.

*Reference information, not medical advice, and not a prediction for any individual. A genetic counselor or clinician can interpret what it means for you and your family.*

|  |  |
| --- | --- |
| Typical inheritance (of this condition) | Autosomal recessive |
| Age of onset (of this condition) | All ages |
| Prevalence | 1-9 / 1 000 000 (United States) |
| Diagnostic panels | XPC is a diagnostic-grade gene on 8 Genomics England panels |

**Commonly reported features of Xeroderma pigmentosum** (across patients with this condition; presentation varies — frequencies from Orphanet):

- Hypogonadism — Very frequent (99-80%)
- Abnormality of the dentition — Very frequent (99-80%)
- Conjunctival telangiectasia — Very frequent (99-80%)
- Optic atrophy — Very frequent (99-80%)
- Dry skin — Very frequent (99-80%)
- Thin skin — Very frequent (99-80%)
- Cutaneous photosensitivity — Very frequent (99-80%)
- Telangiectasia — Very frequent (99-80%)

**Support & next steps:** [Condition overview & support (NIH GARD)](https://rarediseases.info.nih.gov/diseases/0005626/index) · [Find a genetic counselor (NSGC)](https://findageneticcounselor.nsgc.org/).

## Identity {#identity}

| Field | Value |
| --- | --- |
| Gene | [XPC](https://sugi.bio/atlas/gene/XPC/) |
| Protein change (HGVS p.) | p.Ser503= |
| Coding change (HGVS c.) | c.1509C>T |
| MANE Select transcript | [NM_004628](https://www.ncbi.nlm.nih.gov/nuccore/NM_004628) |
| dbSNP | [rs760867012](https://www.ncbi.nlm.nih.gov/snp/rs760867012/) |
| Variant type | single nucleotide variant |
| Location | chr3:14158374-14158374 (GRCh38) |
| ClinVar | [VCV756305](https://www.ncbi.nlm.nih.gov/clinvar/variation/756305/) |

**All HGVS expressions:** `LRG_472:g.25299C>T`, `LRG_472t1:c.1509C>T`, `NC_000003.11:g.14199874G>A`, `NC_000003.12:g.14158374G>A`, `NG_011763.1:g.25299C>T`, `NM_001354726.2:c.930C>T`, `NM_001354727.2:c.1509C>T`, `NM_001354729.2:c.1491C>T`, `NM_001354730.2:c.1509C>T`, `NM_004628.5:c.1509C>T`, `NR_148950.2:n.1542C>T`, `NR_148951.2:n.1418C>T`

## Computational & population evidence {#evidence}

**Concordance:** Mixed / partial computational evidence (see below).

- **Missense predictors (AlphaMissense/REVEL/SaProt) do not apply** to this variant type — they score amino-acid substitutions only. For non-missense variants the computational signal comes from conservation (below), not from a missing predictor score.
- Conservation: phyloP -0.154, GERP -1.56 — not a conserved position (phyloP < 0.1, ACGS BP7 cut)
- CADD: **PHRED 0.903**. No single ClinGen-calibrated threshold exists and the expert panels that use CADD disagree — GUCY2D/AIPL1 require ≥ 20.0 for an untranslated-region variant, ABCA4 ≥ 28.1 for a synonymous or indel variant, the Pulmonary Hypertension panel imports Pejaver 2022's missense-calibrated numbers, and the Antibody Deficiencies panel declines CADD entirely for PIK3CD. CADD v1.7 also incorporates Zoonomia phyloP, so it partly re-expresses the conservation above. *Descriptive; no threshold applied.*
- SpliceAI: **no splice effect predicted**. SpliceAI outputs four numbers per variant, not one: acceptor loss, donor loss, acceptor gain, donor gain (DS_AL / DS_DL / DS_AG / DS_DG). A loss score is an existing splice site weakened or destroyed; a gain score is a new site created or an existing one strengthened. The release publishes its own filter rule, which we read from the dataset rather than assume: an allele is reported only if the largest of its four deltas reaches 0.2. No allele at this position is in the release, so all four are under 0.2 for every alternate allele here. No figure is shown because none was read: the bound is deduced from that absence. It is a result, not a gap in our data, because the release scores every possible substitution across the transcripts it covers (Ensembl MANE v1.4) before it filters, so what survives for a gene is one continuous stretch. What is measured is that this position sits inside the stretch covered for XPC (879 scored positions, the nearest 21 bases away); what is taken from the release's own description, rather than measured, is that coverage inside that stretch is continuous. On that, SpliceAI did score it. *ClinGen's SVI treats the largest of the four as evidence against a splicing effect at or below 0.1, where it may support BP4, and as uninformative between 0.1 and 0.2. We cannot tell which applies here, so these SpliceAI data support neither BP4 nor PP3; that is a statement about this evidence alone, not about the variant's other evidence.*
- Population frequency (gnomAD v4.1): grpmax **0.00636%** (nfe) · FAF95 0.00519% · FAF99 0.00474% · 75/1,179,892 in the highest group · 78/1,613,740 alleles overall — very rare (popmax 0.00636%, nfe).

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| European (non-Finnish) (grpmax) | 0.00636% | 15,732 |
| Finnish (not grpmax-eligible) | 0.00313% | 31,978 |
| Remaining individuals (not grpmax-eligible) | 0.0016% | 62,462 |

*Computational predictors are not independent (ClinGen Variant Classification guidance): AlphaMissense (Cheng et al. 2023) carries the ACMG weight for missense and conservation (phyloP/GERP/phastCons) for non-missense; REVEL (Pejaver-2022 calibrated strength bands) and SaProt (Su et al. 2023, structure-aware, ClinVar-independent protein language model, raw LLR) are shown as orthogonal agreement signals, not additive. For frequency, the gnomAD v4.1 grpmax filtering allele frequency (FAF95) is ClinGen's designated BA1/BS1 input (gnomAD v4 guidance v3.0, June 2025); BA1/BS1 thresholds are disease-specific, not a blanket 5%. Predictions, not a clinical determination.*

## Gene constraint & dosage {#gene-context}

**XPC** population constraint: LOEUF 1.023, pLI 1.2517e-20, missense-Z 0.46534. *Lower LOEUF and higher pLI indicate a gene that tolerates loss-of-function poorly; ClinGen dosage is the curated haploinsufficiency call.*

Curated gene–disease validity (ClinGen):

- **xeroderma pigmentosum group C** — Definitive (AR)

## Protein context {#protein}

Residue **503** lies in the 'disordered' region; the 'interaction with rad23b' region.

AlphaFold model confidence (whole protein): pLDDT 67.67, 40% of residues very-high.

**18 experimental structure(s)** (PDB): [28JM](https://www.rcsb.org/structure/28JM), [28JS](https://www.rcsb.org/structure/28JS), [28JV](https://www.rcsb.org/structure/28JV), [28KE](https://www.rcsb.org/structure/28KE), [2A4J](https://www.rcsb.org/structure/2A4J), [2GGM](https://www.rcsb.org/structure/2GGM).

## What this gene does {#gene-function}

*Describes the biological roles of XPC (the gene this variant disrupts) — not effects measured for this specific variant. A damaging variant is expected to affect these functions and pathways; the degree depends on the variant.*

**How this variant is thought to act:** XPC's established molecular role includes damaged DNA binding. p.Ser503= falls in the disordered region.


### Pathways affected {#pathways}

XPC participates in **3 Reactome pathways** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| [DNA Damage Recognition in GG-NER](https://reactome.org/content/detail/R-HSA-5696394) | curated |
| [Formation of Incision Complex in GG-NER](https://reactome.org/content/detail/R-HSA-5696395) | curated |
| [SUMOylation of DNA damage response and repair proteins](https://reactome.org/content/detail/R-HSA-3108214) | curated |

### Molecular function & processes (GO — experimentally supported) {#go}

**Molecular function:** damaged DNA binding, single-stranded DNA binding, transcription coactivator activity, protein-containing complex binding, DNA damage sensor activity.

**Biological process:** nucleotide-excision repair, positive regulation of DNA-templated transcription, UV-damage excision repair, regulation of mitotic cell cycle phase transition.

## Clinical significance {#significance}

**Conflicting classifications of pathogenicity** — review status Conflicting submitters *(criteria provided, conflicting classifications)*, last evaluated 2025-12-01.

**Submitter consensus:** conflicting (4 Likely benign, 1 Uncertain significance, 1 Benign).

**Submission history:** 6 submissions (2018–2025); classifications have differed over time.

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Illumina Laboratory Services, Illumina | Uncertain significance | criteria provided, single submitter | clinical testing | 2018-01-12 |
| Sema4, Sema4 | Likely benign | criteria provided, single submitter | curation | 2021-09-21 |
| Laboratory of Genetics, Children's Clinical University Hospital Latvia | Benign | criteria provided, single submitter | clinical testing | 2025-02-16 |
| Labcorp Genetics (formerly Invitae), Labcorp | Likely benign | criteria provided, single submitter | clinical testing | 2025-11-24 |
| CeGaT Center for Human Genetics Tuebingen | Likely benign | criteria provided, single submitter | clinical testing | 2025-12-01 |
| Blueprint Genetics | Likely benign | criteria provided, single submitter | clinical testing | 2024-07-18 |

## Associated conditions {#conditions}

[xeroderma pigmentosum group C](https://sugi.bio/atlas/disease/xeroderma-pigmentosum-group-c/), [xeroderma pigmentosum](https://sugi.bio/atlas/disease/xeroderma-pigmentosum/).

**Reported phenotype names (ClinVar):** Xeroderma pigmentosum, group C, not provided, Xeroderma pigmentosum, not specified, none provided, XPC-Related Xeroderma Pigmentosum, XERODERMA PIGMENTOSUM III, XP, GROUP C, Xeroderma pigmentosum, complementation group C, AllHighlyPenetrant.

## Similar variants {#similar}

Related XPC variant pages (same residue, condition, or type): [XPC c.104-2A>G](/variant/xpc-c-104-minus-2a-g), [XPC c.1872+1G>A](/variant/xpc-c-1872-plus-1g-a), [XPC c.1872+1G>C](/variant/xpc-c-1872-plus-1g-c), [XPC c.2033+1G>A](/variant/xpc-c-2033-plus-1g-a), [XPC c.2251-1G>C](/variant/xpc-c-2251-minus-1g-c), [XPC c.2420+2T>C](/variant/xpc-c-2420-plus-2t-c), [XPC c.299+1G>A](/variant/xpc-c-299-plus-1g-a), [XPC c.413-24A>G](/variant/xpc-c-413-minus-24a-g).

### Data sources & attribution {#sources}

ClinVar (NCBI — public domain, built 2026-10-14); gnomAD v4.1 (Broad Institute, built 2026-10-15); AlphaMissense (Cheng et al. 2023, © Google DeepMind — CC BY 4.0, built 2026-01-27); REVEL (Ioannidis et al. 2016 — ODbL, built 2026-07-13); SaProt (Su et al. 2023 — MIT, built 2026-10-14); SpliceAI (Illumina — free for non-commercial use, built 2026-10-13); CADD (Rentzsch et al. 2019, University of Washington — free for non-commercial use, built 2026-10-10); Conservation (phyloP/phastCons/GERP) (UCSC hg38 470-way mammal (Hiller Lab) + Ensembl Compara, built 2026-07-12); gnomAD Non-coding Constraint (Gnocchi) (Chen et al. 2024, Broad Institute — CC0, built 2026-10-11); gnomAD Regional Missense Constraint (Broad Institute — CC0, built 2026-10-13); Pangolin (Zeng & Li 2022 — CC BY 4.0, built 2026-10-11); Repeat regions (UCSC — RepeatMasker, TRF, segmental duplications, built 2026-10-11); ClinGen (ClinGen, built 2026-09-22); UniProt (CC BY 4.0); Reactome / GO (CC BY 4.0, built 2026-09-23); MaveDB (per-record license, built 2026-10-11); CIViC (CC0, built 2026-09-22); Orphanet (Orphanet, built 2026-06-12)

*Primary record: NCBI ClinVar (variation 756305). Classifications reflect these databases as of the page's build date and may change. Free reference use — not medical advice; consult the primary submitters and a clinician.*