Is C5AR1 p.Ser271= (c.813G>A) pathogenic?

C5AR1 p.Ser271= (c.813G>A) is classified Likely benign in C5AR1 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2023-09-04). Very rare (popmax 0.00329%, sas); Associated with C5AR1-related disorder.

What condition is associated with C5AR1 p.Ser271= (c.813G>A)?

C5AR1 p.Ser271= (c.813G>A) is associated with C5AR1-related disorder (ClinVar).

How common is C5AR1 p.Ser271= (c.813G>A) in the general population?

C5AR1 p.Ser271= (c.813G>A) is very rare (popmax 0.00329%, sas) (gnomAD).

C5AR1 p.Ser271=

c.813G>A · rs948785923 · VCV3051110

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00329%, sas)

Conditions

C5AR1-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -1.8	GERP -3.8
Overall
CADD	0.51	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00329% South Asian · 3/91,074 alleles

Filtering AF 0.000875% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000443%

Overall 0.000991% 16/1,613,782 alleles · very rare exomes 13/1,461,832 · genomes 3/151,950 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.00329%	30,358
East Asian	0.00223%	44,872
Remaining individualsnot grpmax-eligible	0.0016%	62,480
African / African-American	0.00134%	74,846
European (non-Finnish)	0.000847%	117,996

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: C5AR1
Protein: p.Ser271=
Coding: c.813G>A
MANE Select: NM_001736
dbSNP: rs948785923
Type: single nucleotide variant
Location: chr19:47320590 (GRCh38)
Gene constraint: LOEUF 1.779 · pLI 0.38 (gnomAD)
Structure: AlphaFold pLDDT 85.57 · 21 PDB
Residue 271: a β-strand

Full C5AR1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

C5AR1-related disorder

Similar variants

C5AR1 p.Ser271Leu Uncertain significance ★ ⚠ same residue
C5AR1 p.Ser271Trp Uncertain significance ★ ⚠ same residue
C5AR1 p.Gly106Arg Uncertain significance ★★ ⚠ same condition
C5AR1 p.Arg34Cys Uncertain significance ★ ⚠ same condition
C5AR1 p.Pro170His Uncertain significance ★ ⚠ same condition
C5AR1 p.Lys313fs Uncertain significance same condition
C5AR1 p.Glu179= Likely benign ★★ same type
C5AR1 p.Thr219= Likely benign ★★ same type

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/c5ar1-p-ser271 (accessed [today's date]).

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