Is CD68 p.Ser258Leu (c.773C>T) pathogenic?

CD68 p.Ser258Leu (c.773C>T) is classified Uncertain significance in CD68 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-11-03). AlphaMissense: likely benign (0.0666); Rare (popmax 0.575%, mid).

How common is CD68 p.Ser258Leu (c.773C>T) in the general population?

CD68 p.Ser258Leu (c.773C>T) is rare (popmax 0.575%, mid) (gnomAD).

What do computational predictors say about CD68 p.Ser258Leu (c.773C>T)?

AlphaMissense predicts likely benign (score 0.0666) — an in-silico prediction, not a clinical call.

CD68 p.Ser258Leu

c.773C>T · rs779654567 · VCV3140651

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0666 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.575%, mid)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0666	likely benign
REVEL	0.102	moderately benign-leaning
SaProt	LLR -8.62	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.002	GERP -4.5, phastCons 0.001
Regional constraint	o/e 1.04	unconstrained · MANE · 1,830 bp · p 0.38 · regional, not allelic
Overall
CADD	14.0	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.575% Middle Eastern · 35/6,084 alleles

Filtering AF 0.425% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.373%

Overall 0.0126% 203/1,613,850 alleles · rare

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.575%	174
African / African-American	0.0468%	2,138
Admixed American	0.025%	3,999
Remaining individualsnot grpmax-eligible	0.0224%	4,463
South Asian	0.0176%	5,692
European (non-Finnish)	0.00737%	13,563
Finnishnot grpmax-eligible	0.00156%	64,010

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: CD68
Protein: p.Ser258Leu
Coding: c.773C>T
MANE Select: NM_001251
dbSNP: rs779654567
Type: single nucleotide variant
Location: chr17:7580908 (GRCh38)
Gene constraint: LOEUF 1.013 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 74.23

Full CD68 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CD68 p.Ile329Thr Benign ★★ same type
CD68 p.Ala10Val Uncertain significance ★ ⚠ same type
CD68 p.Ala262Thr Uncertain significance ★ ⚠ same type
CD68 p.Ala269Val Uncertain significance ★ ⚠ same type
CD68 p.Ala299Asp Uncertain significance ★ ⚠ same type
CD68 p.Ala99Thr Uncertain significance ★ ⚠ same type
CD68 p.Arg345Pro Uncertain significance ★ ⚠ same type
CD68 p.Arg345Trp 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/cd68-p-ser258leu (accessed [today's date]).

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