Is CP p.Gly707= (c.2121C>T) pathogenic?

CP p.Gly707= (c.2121C>T) is classified Likely benign in CP (ClinVar, Single submitter, 1 submitter; last evaluated 2023-04-01). Very rare (popmax 0.00878%, sas).

How common is CP p.Gly707= (c.2121C>T) in the general population?

CP p.Gly707= (c.2121C>T) is very rare (popmax 0.00878%, sas) (gnomAD).

CP p.Gly707=

c.2121C>T · rs771501394 · VCV2654216

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00878%, sas)

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
Pangolin	Δ0.30	loss · gain 0.11 · not in the SpliceAI release · independent
Constraint at this position
Conservation	phyloP -6.8	GERP -4.4
Overall
CADD	1.197	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00878% South Asian · 8/91,072 alleles

Filtering AF 0.00437% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00312%

Overall 0.00118% 19/1,613,908 alleles · very rare

Ancestry group	Frequency	1 in
Ashkenazi Jewishnot grpmax-eligible	0.0101%	9,867
South Asiangrpmax	0.00878%	11,384
Admixed American	0.00167%	59,976
European (non-Finnish)	0.000593%	168,572

Ashkenazi Jewish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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: CP
Protein: p.Gly707=
Coding: c.2121C>T
MANE Select: NM_000096
dbSNP: rs771501394
Type: single nucleotide variant
Location: chr3:149185403 (GRCh38)
Gene constraint: LOEUF 0.624 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 93.79 · 4 PDB
Residue 707: the plastocyanin-like 4 domain; a disulfide bond

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

Similar variants

CP p.Gly707Ser Uncertain significance ★ ⚠ same residue
CP c.1208+1G>A Pathogenic ★★ same type
CP c.2879-1G>T Likely pathogenic ★★ same type
CP p.Arg901Ter Pathogenic ★★ same type
CP p.Gly195Arg Likely pathogenic ★★ same type
CP p.Gly650Arg Pathogenic/Likely pathogenic ★★ same type
CP p.Gly708Ser Pathogenic ★★ same type
CP p.Leu919Pro Pathogenic/Likely pathogenic ★★ 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/cp-p-gly707 (accessed [today's date]).

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