# NM_004628.5(XPC):c.303C>T (p.Asp101=)

https://sugi.bio/variant/xpc-p-asp101

## Summary

**XPC p.Asp101= (c.303C>T)** is classified **Benign** in XPC (ClinVar, Multiple submitters, 4 submitters; last evaluated 2026-02-04). Low-frequency (popmax 1.81%, sas); Associated with xeroderma pigmentosum group C.

**At a glance:** Benign · review: Multiple submitters · rsID rs41545713 · 4 submitters · 1 linked condition · low-frequency (popmax 1.81%, sas)

## For patients & families {#patients}

This is a change in the XPC gene that is classified as benign — not considered disease-causing, submitted by 4 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.Asp101= |
| Coding change (HGVS c.) | c.303C>T |
| MANE Select transcript | [NM_004628](https://www.ncbi.nlm.nih.gov/nuccore/NM_004628) |
| dbSNP | [rs41545713](https://www.ncbi.nlm.nih.gov/snp/rs41545713/) |
| Variant type | single nucleotide variant |
| Location | chr3:14170547-14170547 (GRCh38) |
| ClinVar | [VCV695695](https://www.ncbi.nlm.nih.gov/clinvar/variation/695695/) |

**All HGVS expressions:** `LRG_472:g.13126C>T`, `LRG_472t1:c.303C>T`, `NC_000003.11:g.14212047G>A`, `NC_000003.12:g.14170547G>A`, `NG_011763.1:g.13126C>T`, `NM_001354726.2:c.-153C>T`, `NM_001354727.2:c.303C>T`, `NM_001354729.2:c.285C>T`, `NM_001354730.2:c.303C>T`, `NM_004628.5:c.303C>T`, `NR_148950.2:n.336C>T`, `NR_148951.2:n.336C>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 2.119, GERP -0.733, phastCons 0.419 — highly conserved position (PP3-type support)
- CADD: **PHRED 4.778**. 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: **not assessed** — no allele at this position is in our SpliceAI release, either because it lies outside the scored MANE transcript scope or because every allele is below Δ0.2. We cannot tell which, so this claims neither; absence is not evidence against a splicing effect.
- Population frequency (gnomAD v4.1): grpmax **1.81%** (sas) · FAF95 1.74% · FAF99 1.71% · 1,639/90,492 in the highest group · 3,406/1,610,506 alleles overall — low-frequency (popmax 1.81%, sas).

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| South Asian (grpmax) | 1.81% | 55 |
| Middle Eastern | 0.958% | 104 |
| Remaining individuals (not grpmax-eligible) | 0.239% | 419 |
| European (non-Finnish) | 0.125% | 800 |
| Admixed American | 0.0922% | 1,085 |
| Ashkenazi Jewish (not grpmax-eligible) | 0.0407% | 2,459 |
| African / African-American | 0.02% | 4,995 |
| Finnish (not grpmax-eligible) | 0.00469% | 21,315 |
| East Asian | 0.00447% | 22,390 |

*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}


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.


### 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}

**Benign** — review status Multiple submitters *(criteria provided, multiple submitters, no conflicts)*, last evaluated 2026-02-04.

**Submitter consensus:** unanimous (4/4 Benign).

**Submission history:** 4 submissions (2017–2026); classifications have been stable.

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Labcorp Genetics (formerly Invitae), Labcorp | Benign | criteria provided, single submitter | clinical testing | 2026-02-04 |
| Illumina Laboratory Services, Illumina | Benign | criteria provided, single submitter | clinical testing | 2017-04-27 |
| Genome-Nilou Lab | Benign | criteria provided, single submitter | clinical testing | 2021-12-05 |
| Breakthrough Genomics, Breakthrough Genomics | Benign | criteria provided, single submitter | not provided |  |

## Associated conditions {#conditions}

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

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

## 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 2026-10-14); 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 695695). 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.*