Is CCS p.Arg71Trp (c.211C>T) pathogenic?

CCS p.Arg71Trp (c.211C>T) is classified Uncertain significance in CCS (ClinVar, Single submitter, 1 submitter; last evaluated 2022-01-10). AlphaMissense: likely benign (0.1787); Ultra-rare (popmax 0.0134%, nfe).

How common is CCS p.Arg71Trp (c.211C>T) in the general population?

CCS p.Arg71Trp (c.211C>T) is ultra-rare (popmax 0.0134%, nfe) (gnomAD).

What do computational predictors say about CCS p.Arg71Trp (c.211C>T)?

AlphaMissense predicts likely benign (score 0.1787) — an in-silico prediction, not a clinical call.

CCS p.Arg71Trp

c.211C>T · rs763610047 · VCV2271573

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1787 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0134%, nfe)

Missense predictors

2/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1787	likely benign
REVEL	0.868	moderately pathogenic-leaning
SaProt	LLR -11.80	damaging
⇒ REVEL and SaProt call this damaging; AlphaMissense does not.
Splicing
SpliceAI	Δ0.21	donor gain · deltas
Constraint at this position
Conservation	phyloP 2.2	GERP -1, phastCons 1
Regional constraint	o/e 0.91	unconstrained · MANE · 13 kb · p 0.085 · regional, not allelic
Overall
CADD	27.7	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 0.0134% European (non-Finnish) · 158/1,179,430 alleles

Filtering AF 0.0117% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.011%

Overall 0.0101% 163/1,612,540 alleles · ultra-rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.0134%	7,465
Remaining individualsnot grpmax-eligible	0.0032%	31,209
Admixed American	0.00167%	59,772
African / African-American	0.00134%	74,820
South Asian	0.0011%	90,970

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: CCS
Protein: p.Arg71Trp
Coding: c.211C>T
MANE Select: NM_005125
dbSNP: rs763610047
Type: single nucleotide variant
Location: chr11:66599214 (GRCh38)
Gene constraint: LOEUF 1.193 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 87.54 · 7 PDB
Residue 71: the hma domain; a β-strand

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

Similar variants

CCS c.567+1G>C Uncertain significance ★ same type
CCS p.Ala173Thr Uncertain significance ★ ⚠ same type
CCS p.Ala179Thr Uncertain significance ★ ⚠ same type
CCS p.Ala234Thr Uncertain significance ★ ⚠ same type
CCS p.Ala260Ser Uncertain significance ★ ⚠ same type
CCS p.Ala260Thr Uncertain significance ★ ⚠ same type
CCS p.Arg163Gln Uncertain significance ★ ⚠ same type
CCS p.Arg163Gly Uncertain significance ★ ⚠ 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/ccs-p-arg71trp (accessed [today's date]).

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