Is XPC p.Arg155= (c.465A>G) pathogenic?

XPC p.Arg155= (c.465A>G) is classified Likely benign in XPC (ClinVar, Multiple submitters, 2 submitters; last evaluated 2023-12-05). Very rare (popmax 0.00559%, nfe); Associated with xeroderma pigmentosum.

What condition is associated with XPC p.Arg155= (c.465A>G)?

XPC p.Arg155= (c.465A>G) is associated with xeroderma pigmentosum (ClinVar).

How common is XPC p.Arg155= (c.465A>G) in the general population?

XPC p.Arg155= (c.465A>G) is very rare (popmax 0.00559%, nfe) (gnomAD).

How is Xeroderma pigmentosum inherited?

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

XPC p.Arg155=

c.465A>G · rs370322435 · VCV755988

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00559%, nfe)

Conditions

xeroderma pigmentosum

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · T>A here scores Δ0.24 · evaluated, not missing
Constraint at this position
Conservation	phyloP -3.8	GERP -3.4
Overall
CADD	2.397	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00559% European (non-Finnish) · 66/1,179,872 alleles

Filtering AF 0.00451% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00411%

Overall 0.00421% 68/1,613,832 alleles · very rare exomes 65/1,461,656 · genomes 3/152,176 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00559%	17,877
Admixed American	0.00333%	29,999

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.Arg155=
Coding: c.465A>G
MANE Select: NM_004628
dbSNP: rs370322435
Type: single nucleotide variant
Location: chr3:14168328 (GRCh38)
Gene constraint: LOEUF 1.023 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 67.67 · 18 PDB

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

Disease context

xeroderma pigmentosum — 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.Arg155Ter Pathogenic ★★ same residue
XPC p.Arg155Gln Conflicting classifications of pathogenicity ★ ⚠ same residue
XPC c.2033+1G>A Pathogenic/Likely pathogenic ★★ same condition
XPC c.2251-1G>C Pathogenic ★★ same condition
XPC c.621+1G>A Likely pathogenic ★★ same condition
XPC c.622-2A>C Pathogenic ★★ same condition
XPC p.Arg220Ter Pathogenic ★★ same condition
XPC p.Arg293Ter 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-arg155 (accessed [today's date]).

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