Is CD7 p.Lys206Asn (c.618G>C) pathogenic?

CD7 p.Lys206Asn (c.618G>C) is classified Uncertain significance in CD7 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-10-02). AlphaMissense: likely pathogenic (0.7109); Ultra-rare (popmax 0.0535%, eas).

How common is CD7 p.Lys206Asn (c.618G>C) in the general population?

CD7 p.Lys206Asn (c.618G>C) is ultra-rare (popmax 0.0535%, eas) (gnomAD).

What do computational predictors say about CD7 p.Lys206Asn (c.618G>C)?

AlphaMissense predicts likely pathogenic (score 0.7109) — an in-silico prediction, not a clinical call.

CD7 p.Lys206Asn

c.618G>C · rs760915399 · VCV3140655

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.7109 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0535%, eas)

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.7109	likely pathogenic
REVEL	0.05	moderately benign-leaning
SaProt	LLR -8.51	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 1.1	GERP -0.22, phastCons 0.001
Regional constraint	o/e 0.89	unconstrained · MANE · 2,171 bp · p 0.046 · regional, not allelic
Overall
CADD	21.9	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 0.0535% East Asian · 24/44,890 alleles

Filtering AF 0.0368% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0313%

Overall 0.00174% 28/1,613,510 alleles · ultra-rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0535%	1,870
Remaining individualsnot grpmax-eligible	0.0048%	20,821
South Asian	0.0011%	91,080

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: CD7
Protein: p.Lys206Asn
Coding: c.618G>C
MANE Select: NM_006137
dbSNP: rs760915399
Type: single nucleotide variant
Location: chr17:82315426 (GRCh38)
Gene constraint: LOEUF 1.673 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 77.51 · 2 PDB

Full CD7 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CD7 p.Ala145Thr Uncertain significance ★ ⚠ same type
CD7 p.Ala154Asp Uncertain significance ★ ⚠ same type
CD7 p.Ala154Thr Uncertain significance ★ ⚠ same type
CD7 p.Ala15Val Uncertain significance ★ ⚠ same type
CD7 p.Ala17Ser Uncertain significance ★ ⚠ same type
CD7 p.Ala184Val Uncertain significance ★ ⚠ same type
CD7 p.Ala217Thr Uncertain significance ★ ⚠ same type
CD7 p.Ala218Thr 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/cd7-p-lys206asn (accessed [today's date]).

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