Is XPC p.Phe287Cys (c.860T>G) pathogenic?

XPC p.Phe287Cys (c.860T>G) is classified Benign/Likely benign in XPC (ClinVar, Multiple submitters, 9 submitters; last evaluated 2026-02-04). AlphaMissense: likely pathogenic (0.7111); Low-frequency (popmax 2.11%, afr); Associated with xeroderma pigmentosum group C.

What condition is associated with XPC p.Phe287Cys (c.860T>G)?

XPC p.Phe287Cys (c.860T>G) is associated with xeroderma pigmentosum group C (ClinVar).

How common is XPC p.Phe287Cys (c.860T>G) in the general population?

XPC p.Phe287Cys (c.860T>G) is low-frequency (popmax 2.11%, afr) (gnomAD).

How is Xeroderma pigmentosum inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

What do computational predictors say about XPC p.Phe287Cys (c.860T>G)?

AlphaMissense predicts likely pathogenic (score 0.7111) — an in-silico prediction, not a clinical call.

XPC p.Phe287Cys

c.860T>G · rs35629274 · VCV135482

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 9 submitters

AlphaMissense

likely pathogenic

0.7111 · ACMG-weighted

gnomAD v4.1

Rare

low-frequency (popmax 2.11%, afr)

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

xeroderma pigmentosum group C

Computational evidence

Protein change
AlphaMissense	0.7111	likely pathogenic
REVEL	0.199	benign-leaning
SaProt	LLR -8.87	tolerated
⇒ AlphaMissense calls this damaging; REVEL and SaProt do not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 11	GERP 1.5, phastCons 1
Regional constraint	o/e 0.97	unconstrained · MANE · 33 kb · p 0.33 · regional, not allelic
Overall
CADD	25.4	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 2.11% African / African-American · 1,580/74,998 alleles

Filtering AF 2.02% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.99%

Overall 0.109% 1,756/1,613,286 alleles · low-frequency exomes 864/1,461,008 · genomes 892/152,278 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	2.11%	47
Remaining individualsnot grpmax-eligible	0.123%	811
Admixed American	0.105%	952
Middle Eastern	0.0991%	1,009
Ashkenazi Jewishnot grpmax-eligible	0.00338%	29,592
South Asian	0.0033%	30,304
European (non-Finnish)	0.00212%	47,183
Finnishnot grpmax-eligible	0.00156%	63,998

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: XPC
Protein: p.Phe287Cys
Coding: c.860T>G
MANE Select: NM_004628
dbSNP: rs35629274
Type: single nucleotide variant
Location: chr3:14164853 (GRCh38)
Gene constraint: LOEUF 1.023 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 67.67 · 18 PDB
Residue 287: a UniProt-annotated variant site (in)

Full XPC gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

xeroderma pigmentosum group C — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Xeroderma pigmentosum (Orphanet):

Inheritance: Autosomal recessive
Onset: All ages
Prevalence: 1-9 / 1 000 000 (United States)

Similar variants

XPC p.Phe287Leu Uncertain significance ★ ⚠ same residue
XPC c.104-2A>G Likely pathogenic ★★ same condition
XPC c.1872+1G>A Likely pathogenic ★★ same condition
XPC c.1872+1G>C Pathogenic/Likely pathogenic ★★ same condition
XPC c.2033+1G>A Pathogenic/Likely pathogenic ★★ same condition
XPC c.2251-1G>C Pathogenic ★★ same condition
XPC c.2420+2T>C Pathogenic/Likely pathogenic ★★ same condition
XPC c.299+1G>A Likely pathogenic ★★ same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/xpc-p-phe287cys (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown